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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact...

Basic information

species Zea mays
transcript GRMZM2G028432_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G07980.1 (Glycine max), 5'ss of exon 1
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact-----
|||| |||||||| || ||||| || |||||||| || || || || ||||| ||  | || ||||||||||||||||| ||||| ||||| ||||| ||||    |  ||  ||| | |  |||| | || | |  |||   ||     || ||    |       | |  ||   ||||      |     ||    |     
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCGCTTGCGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGATGCCGGTGTTAGgt----attctcactcattttctatttttctttttctttttacttataacatgatcgaataagatgcgta-tagttataattattttcttgcgtatggttaggta

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G05630.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgata-atatgctggtcaatgcagcagcagtaatg-gcaggcac-ttctaaaact--
|||||||||| || || ||||| || || || || || ||||| || ||||| ||  | || ||||||||||| ||||||||||| ||||| ||||| |||||   |   |   ||  ||   ||   |||    | | | | |  |||| |  ||    |    ||||| |    | | ||| || ||    || |  || |  
TCTTTGACGGTTACGCGCACCTCTCTTCGGGTCTCGCTTGTGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattca---tcattcaaattcaatcaagcttcgagttgttgct--gctgctttatgctttcactaatgctgtttgattgatgtgctggtgtgttttgtaattca

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G11760.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttg--gtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact
||||||| || ||||| || || || || || ||||||||||| || ||||| ||  |||| |||||||| ||||| || ||||||||||||||||| ||||| |     |  ||  |  | |    |  ||| |  | ||   ||   ||    |  | ||| |     ||       || |  || |   | |||     
TCTTTGATGGTTATGCACATCTCTCCTCTGGTCTTGCCTGTGGGCTGGCTGGCCTCTCTGCTGGCATGGCTATTGGTATTGTTGGTGATGCTGGTGTTAGgtataattcttctcttctgccttgccttagtatcttatctgtaattaaacttgatacttactgatttgatcactgtttttactcacatgatttgctatgc--

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G03470.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctc-ttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact--------
||||||| || ||||| ||  |||| || |||||||||||||| || ||||| ||  |||| || ||||||||||| || ||||||||||||||||||||||||      ||| || | ||||| |  ||  |      | ||     ||  ||  ||| | |    || || |  |||  ||| ||   ||| ||    |        
TCTTTGATGGATATGCTCATTTGTCCTCTGGCCTTGCCTGTGGCCTAGCTGGCCTCTCTGCTGGAATGGCCATTGGGATTGTTGGTGATGCTGGTGTCAGgtaattgtaattcatcatcatcatgtcatgtcaagcctatgggc---acttgtagaatgttag---gtgtagta--agttttgg-agatccttatattgattagtgata

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA14G23990.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgc-agcagcagtaatggcaggcacttctaaaact---
||||||| |||||||||||| |||| || ||||| |||||||| || ||||| ||  |||| || ||||||||||| || ||||||||||||||||||||||||      ||| | ||    |||  || |  ||||  || | || ||    | |   |  | ||||  ||  | |||||  |  ||   |  | | | |   
TCTTTGATGGCTATGCCCACTTGTCCTCTGGCCTCGCCTGTGGCCTCGCTGGCCTCTCTGCTGGAATGGCCATTGGGATTGTTGGTGATGCTGGTGTCAGgtaattgttattcattttcat-tatcatgat-catgccatg-tatgcctatggacac-ttcttgaatgttaggtgtagtaagtgttggagatctttatattgat

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G24220.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcc--tcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggc--acttctaaaact
| ||||||||||| |||||||| || || || || || ||||| || ||||| ||  | || ||||||||||| ||||||||||| ||||| ||||| |||||   |   ||    | | |||||  |  |   |||   ||| |   |||  | || |  |  | ||||  |||    |  ||   ||   |    |  |   
TTTTTGACGGCTACGCCCACCTCTCTTCAGGTCTCGCTTGTGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatcatttaaatttaatcatgcttcgagttat-tgttgctgctgct--ttatgttttcattaatgttgcatgcttgttgtttggttgatgggttgagt-

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G04090.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatatt--ctgctatatgctttggtttgg--ctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact
||||||| || ||||| || || || || || ||||||||||| || ||||| ||  |||| |||||||| ||||| || ||||||||||||||||| ||||| |     |    ||||  || ||  ||   ||     | |||   |   ||||  ||| |||     | |||      |  ||  |   | |   |     
TCTTTGATGGTTATGCACATCTCTCCTCTGGTCTTGCCTGTGGGCTGGCTGGTCTCTCTGCTGGCATGGCTATTGGTATTGTTGGTGATGCTGGTGTTAGgtataattcttctgccttagtatcttatctatgattaaactcggtactgatttgatcttattctgaagtctacagatttcatggtgatacttaatgtgat----

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G37320.1 (Glycine max), 5'ss of exon 1
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctct-tatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact
|||| |||||||| || ||||| || ||||||||  | || ||||||||||| ||  | || ||||||||||||||||| ||||| || || ||||| |||||    | || | | | ||   | |  |  | | |         ||  ||    |||  |  |   |   |||   |   ||| |     ||| |   | 
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCTCTTGCGGTCTTGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGACGCCGGTGTTAGgtattctcactccttttctactctctctttttctttcgaaaaagatgcgtgtagttataattattt-tcttgcatatggtttggtatttggttcaaggcca

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G00950.2 (Glycine max), 5'ss of exon 1
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtt--tggctgataatatgct---ggtca-atgcagcagcagtaatg-gcaggcacttctaaaact
||||||| || ||||| || || || || || |||||||||||  | ||||| ||| |||| |||||||| ||||| || || |||||||||||||| ||||| | | ||||  |    |  | || |  |||||| |||| ||  |   |  | || || |   ||||   |  |   ||| || ||   ||  || |  |     
TCTTTGATGGTTATGCACATCTCTCCTCTGGTCTTGCCTGTGGCTTGGCTGGCCTTTCTGCTGGCATGGCTATTGGTATTGTCGGTGATGCTGGTGTTAGgtata-atgcttttttactttgt-ttttcatatatgatttgtttcttatttcttgatgtgtttaaggtcttgttgaattgcaatattgcatagtgacattca-----

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G00980.1 (Glycine max), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact----
||||||| || ||||| || || || || || |||||||||||  | ||||| ||| |||| |||||||| ||||| || ||||||||||| ||||| ||||| | | || |  |    |  | |  | || | ||  |   ||  | |  || |    ||  ||||   |||  ||| |       | |||     |||    
TCTTTGATGGTTATGCACATCTCTCTTCTGGTCTTGCCTGTGGCTTGGCTGGCCTTTCTGCTGGCATGGCTATTGGTATTGTTGGTGATGCCGGTGTTAGgtacaaaagcctttttactttgtttcttact-tctgtatgttttaaggtcttattgaattg--caatattgca-tagtgacactcaactcttgatccactgact

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatat-gctggtcaatgcagcagcagtaatggcaggcacttctaaaact---
| || || |||||||| || || || || || || || |||||||||||||| ||  |||| || ||||| ||||| ||||| |||||||||||||| ||||||    |||  ||||    | ||  |  ||  || ||   |   ||   |   || | |  ||| |     || |||    | ||  |  | |     |   
TATTCGATGGCTATGCTCATCTCTCTTCTGGGCTAGCTTGTGGTCTTGCTGGTCTCTCTGCTGGTATGGCTATTGGAATCGTCGGTGATGCTGGTGTTAGgtaa--ttgctatctct-gctacatgatcttaactgtttgattgcagcaattttgatcgattttcacttgtttagaagtttctg-agatagctttgttgtttgt

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT2G16510.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctat---atgctttggtttggctgataatatg-ctggtcaatgcagcagcagtaatggcaggcacttctaaaact
| |||||||| || || ||||| ||||| || ||||| |||||||||||||| ||  | || || ||||| ||||| || ||||||||||| ||||| ||||        ||||||  |    ||  |   ||   |  | ||    |      ||   || || ||   ||     ||  |  |  |||              
TATTTGACGGATACGCTCACCTTTCGTCTGGTCTTGCTTGTGGTCTTGCTGGACTCTCAGCTGGTATGGCTATTGGAATTGTTGGTGATGCGGGTGTTAGgtttg-----ttcctcacagagaatgtttgaatggaaaacgttaacgtcatctgtatcttgacttgtttttggttttgcgattctctcag--------------

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact-------
|||| ||||| ||||| || || || || || ||||| ||||| || ||||| ||| | || || |||||||| || |||||||| ||||||||||||||||    ||| | |    | || |  | ||| | || |  |  | | ||   |||| ||||     |  ||     |   | |     | |   ||  | |       
TCTTCGACGGATATGCTCATCTCTCTTCTGGTCTTGCTTGTGGGCTAGCTGGTCTTTCAGCTGGAATGGCCATAGGTATCGTTGGCGATGCTGGTGTCAGgt----acgatcctctgtgtccttctttgc-agattcactcttatagcc--taatttgctaaaagactcaattttatacaagtatatctcccttatgaatcagaata

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT4G34720.1 (Arabidopsis thaliana), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaat-ggcaggcacttctaaaact---------
||||||| || || || || || ||||| || ||||| |||||||||||||| ||  | || || ||||||||||| || ||||||||||| ||||||||||        |  ||||  || |   ||||||  || |  | ||||   | || ||||   |  | || | ||   ||  | | |   | ||| |   | |         
TCTTTGATGGATACGCACATCTCTCGTCTGGTCTTGCTTGTGGTCTTGCTGGTCTCTCAGCTGGAATGGCCATTGGGATTGTTGGTGATGCCGGTGTCAGgt-------ttgtctctcgtcct--cctgctac-tgatacgctttga--ggtattatggaagata-tgtaacattggtgtttgacttacccttttgcgattctttttcag

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgta-------aagacgcttcctcttatcatattctgctatatgctttg--gtttg-gctgataatatgctggtcaatgcagcagcagtaatggcag-gcacttctaaaact---------------------------------------------------------------------------
| || |||||||| || ||||| || || ||  |  | |||||  | ||||| ||  | ||||||||||||||||| ||||| || ||||||||||| |||||       ||| |      | |    || | |    ||| | ||||  ||| | |   ||| | |||   ||        |   |||  |||    |  |  |  |  |                                                                           
TGTTCGACGGCTACGCGCACCTTTCATCTGGATTGTCGTGTGGGTTGGCTGGTCTATCGGCAGGCATGGCCATTGGTATCGTCGGAGATGCTGGTGTTAGgtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcag

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S2_120V6.1 (Physcomitrella patens), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattc-tgctatatgctt------tggtttggctgataa--------tatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact----------------------------------------------------------
| || ||||||||||| ||||| || || ||  |  | || ||||| ||||| ||  | || |||||||||||||| || ||||| |||||||| |||||||||  |  |    ||| | || ||   |   | |||  |      | | |||  || | |        | |  |  || || ||    |||   || |       ||  || ||                                                          
TGTTCGACGGCTATGCTCACCTTTCATCTGGTTTGTCGTGCGGTCTAGCTGGTCTGTCCGCTGGCATGGCCATTGGTATTGTTGGAGATGCTGGGGTCAGgtaataattcaagatctgagcacatctataagaaatgtgtaacacataggttgaatggtgaatcttgtctcttttcttcgattcaaattcagagctgacttttggatcataacctaccattggtaaatacatgcacgggggtttgaccggagggtttatttttttgtgcgcag

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact-----------------------------------------------------------------------------------------------------
| ||||||||||| || || || || || ||  |  | || ||  | || || ||  | |||||||||||||| || |||||||| ||||||||||| |||||  |   |   | |||   || |  || | ||||        | | |||   |     |    ||| |   |   |       |   |    |    |                                                                                                     
TGTTTGACGGCTACGCGCATCTTTCATCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcgg-acgaacccttgcaatgtggtgatgtatgggaatacgtag-tgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttgtgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact-----------------------------------------------------------------------------------------------------
| ||||||||||| || || || || || ||  |  | || ||  | || || ||  | |||||||||||||| || |||||||| ||||||||||| |||||  |   |   | |||   || |  || | ||||        | | |||   |     |    ||| |   |   |       |   |    |    |                                                                                                     
TGTTTGACGGCTACGCGCATCTTTCTTCGGGATTGTCTTGCGGGTTGGCAGGACTGTCGGCAGGCATGGCCATCGGTATCGTTGGAGATGCTGGTGTGAGgtagcgg-acgaacccttgcaatgtggtgatgtatgggaatacgtag-tgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcag

upper sequence: GRMZM2G028432_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S1_66V6.1 (Physcomitrella patens), 5'ss of exon 2
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctct------tatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagca-gtaatggcaggcactt-ctaaaact----------------------------------------------------------------------------
| |||||||||||||| || || || || || ||  | |||||  | || || ||  | ||||||||||| |||||||||||||| |||||||||||||||||   |  |   ||||      |     |||  |   | | ||||  ||   ||  |  | | ||| |  ||       |   |      |   | || ||   | |                                                                            
TGTTTGACGGCTATGCGCATCTTTCATCTGGTCTGTCATGTGGGTTAGCCGGCCTGTCCGCAGGCATGGCGATTGGCATCGTTGGAGATGCTGGTGTCAGgtagtaatcccgtctctacgtttttctgcatttagtatttttctttttttcttcttttttttttctgcttgatatgatttcctattgctttatttattttctgtgaattgccattatgcatcatgtgatgcaatttttgttacctgatgtattctttgaccggattatggttatacgtctgtag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29947353|gb|CB816610.1|CB816610
EST:     GGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAG                         GGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCAT
genomic: GGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgc ... ttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCAT
EST: gi|15427247|gb|BI543069.1|BI543069
EST:     GGGCTTGCTGCAGGCATGGCCATTGGCATCCTTGGTGATGCTGGTGTCAG                         GGCGAACGCTCAGCAGCCAAAGC
genomic: GGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgc ... ttttgcgcagGGCGAACGCTCAGCAGCCAAAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgc ... ttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 348

TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgc ... ttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgc ... ttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgc ... ttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTGACGGCTATGCCCACCTGTCGTCCGGCCTTGCCTGTGGTCTTGCTGGGCTTGCTGCAGGCATGGCCATTGGCATCGTTGGTGATGCTGGTGTCAGgtaaagacgcttcctcttatcatattctgctatatgctttggtttggctgataatatgctggtcaatgcagcagcagtaatggcaggcacttctaaaact

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcctc