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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

Basic information

species Zea mays
transcript GRMZM2G071970_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattc--tttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
 |  || |  |      |   ||  ||||||    | |  ||  |   |    |  |||||       ||    ||||||||| | ||    | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgt---ttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
ttctaatcacag--atagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaaca-gacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   ||| ||  |  || |  ||| || || ||  ||     ||  ||| |  |        | |  |  |   | ||||||||| || |  || ||  |||||||||||||||||||||||||||||| || |||||||||||||||||||||||| |||| |||||||||||||| |||||||| |||||||||||||||||
---taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttctctttattgattcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgt-----ctatattttatagcactgagggttcttaacag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
       || |     ||| |  |||   |   |   ||||     ||| |     | | ||     | |   |   |  |||||||   |  |  ||   ||||||||||||||||||||| ||||||||||| ||||||||||||||||  || ||    |||||||| || |||||||| || |||||  | ||| ||||   
------ccatacgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATAACAATACAGTTGTACC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatt-tccatacaagttgc-agtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    |||   |  |  | ||  |   ||| | || |  ||||   ||| |    |  |  || |||        || ||||||   |||  ||| |  |||||||| |||||| | |||||||| ||||| ||||| || ||||| ||||| |||   |||||||| || |||||||| || |||||||||||  |||| ||
-atgaatagtaatttatgttttgtccattgttcagaagagttaagagtatgaaatccaaattctagattcttttgtacttaacctgcatattttgtg-gcagTGACCTGGAATATTACCTGCACTTATTCTCAATTCCTGGCTCAAAAGACACCAAGTTGCTGTGTTTCCCTCTCATCCTTCTATAATGACACCGTTGTAAA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgt-----ctatattttatagcactgagggttcttaacag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
       || |     ||| |  |||   |   |   ||||     ||| |     | | ||     | |   |   |  |||||||   |  |  ||   ||||||||||||||||||||| ||||||||||| ||||||||||||||||  || ||    |||||||| || |||||||| || ||| |  | ||| ||||   
------ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA----------------------------------------------
                                              || || |  |    | ||   ||      |||||    |||   || |  |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | ||| |||  | ||||||||| || |||||  | ||||| || ||                                              
-------------------------------------------ttattagtatgaaaccca-agttttggtttagcttaatctgcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatttccatacaagttgc-agtttcgtcta-tattttatagca-ctgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   ||  |  | |  |||  ||  ||   |   |   ||||   |||| |  |||  |   |  | || || ||  |     |  |   |  |||||  ||||||||||||||||| || ||||||||||| ||||||||||||||||  || ||    ||||| || || || ||||| || ||||| || ||  ||||   
--ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G22410.1 (Glycine max), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctat--attttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   || |      |  | ||  |   ||| |     | | | ||||||     ||  |  || ||||       || ||||||   |||  ||| ||  ||||||| |||||| | |||||||| ||||| ||||| || ||||| ||| | |||   |||||||| || |||||||| || |||||||||||| | || ||
-aatagtagttatttatgttttgtgcattgctcaggagggttcagtttatgaaatccaaattctagcttctcttgtacttaacctgcatattttgtc-acagTGACCTGGAATATTACCTGCACTTATTCTCAATTCCTGGCTCAAAAGGCACCAAGTTGCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacag-acattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  |  |||   | | | |   ||   |   |   ||  |||  |  | ||    |  | |   |          | | |||||  ||  |  ||   ||||||||||||||||||||| |||||||| || |||||||| ||||| || ||||| || || ||||| || || ||||| || |||||||| ||  ||||   
gcttaaatttaaaacaattgaagtttacagttggtattagtaac--tatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
--ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  ||        | | | | ||  || || ||  ||     |   |     || |   ||||  ||   ||      |||||    |||   || |  |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | |||||||| ||||||||||| || |||||  | ||| | || ||
tatttatgctttatacattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
---ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    |  |||   | | |     |    |   |   |||  ||  |  | ||  |||  | |   |          | |||||||  || |  || | ||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||| || |||||||| || || ||||| || |||||||| ||  ||||   
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaac--tatcagctaattctagcaatctgttatatccttaacat-cacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    | | ||    |||  | | |   |  | | |||| ||  | ||| |  |  | |    |  ||||||  ||           ||||       ||||||| |||||||| || |||||||| || || ||  | |||||||| || ||| | |||||||||||||| ||||| ||||||||  | ||||| ||   
-gtaagttac--tcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatg---aaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
---ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    |   |  ||| || | |   ||| |||||   | |    |     ||     | | ||   |  | | |       |||    | |    |||  |||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||  | || ||||| ||  | ||||| || |||||| |||| || ||   
aggatggcaagacacattgacaatggataatttgtgttcttaatatgcatttaa--agagttctcaagatttaactaatctaatcttcctgtcctatg-gcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC

upper sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
ttctaatcacagatagtcttaggaaaatttc----catacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    |   |  |||  |   ||| || |||          || |   | |||   ||||     |||    |   ||  || |||  |  |   |      |||||||||||||||| || ||||| ||||| ||||| ||  ||||||| || ||  | |||||||| || |||||||| || || ||||||||||||||   
----agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC

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|32849583|gb|CD989264.1|CD989264
EST:     GCCAACAAAGTTTTTCACTGCGGATGGGCGCAGGGTAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|14190871|gb|BG833101.1|BG833101
EST:     TGGGCCGCAGGGTAACCCAAGCTCTAA                         TGCACATGGAATGCTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGAC
genomic: TGGG-CGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTG-ACATGGAATG-TGACCTGCACATATTCCCAATTTCTTGCTCAGAAGAC
EST: gi|31355260|gb|CD439617.1|CD439617
EST:     GCCAACAAAGTTTTTCACTGCGGATGGGCGCAGGGTAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|76932301|gb|DV172999.1|DV172999
EST:     GCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|14190870|gb|BG833100.1|BG833100
EST:     GCCAACAAAGTTTTTCACTGCGGATGGGCGCAGGGTAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTC

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: 160

CTTAAGACTCCAGGCCCTGGGTACACATGTGGGCGTGCTATTGTTGGCAGGCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

CTTAAGACTCCAGGCCCTGGGTACACATGTGGGCGTGCTATTGTTGGCAGGCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 183

CTTAAGACTCCAGGCCCTGGGTACACATGTGGGCGTGCTATTGTTGGCAGGCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 399

CTTAAGACTCCAGGCCCTGGGTACACATGTGGGCGTGCTATTGTTGGCAGGCCAACGAAGTTTTTCTCTGCAGATGGGCGCAGGGTAACCCAAGCTCTAAgtaagttgcc ... ttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
                             tcttaac  putative branch site (score: 399)
                                         ttctttatct  putative PPT
     tctatattttata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

- - aatcaca
- - - - - - - - - - - - - - - -catacaa
- - - - - - - - - - - - - - - - - - - gttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcactga