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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaattaatattgttcagatccgttctctttctcaaactaagaaagaaaagcttggcgttttttcttaaatgttgagtaccaaaatcctag

Basic information

species Zea mays
transcript GRMZM2G126795_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaattaatattgttcagatccgttctctttctcaaactaagaaagaaaagcttggcgttttttcttaaatgttgagtaccaaaatcctag-----
||||||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| || || |||||||||||||||||||| |||||||||||||||| |||||   || || ||  | | ||   | |  |  |  ||| ||||||| ||| ||||  ||    ||||   |   | || ||           
AGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAGgtatttgcaaatttcaatggtacaactacttttgttattcccga--aagcaagaaaa-ctttgcgtagttctcaaaatacagtaaaacataacttggatatat

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaa-attaatattgttcagatccgttct--ctttctcaaactaagaaagaaaagcttggcgttttttct-taaatgttgag-taccaaaatcctag
||| | |||||||||||||||||||| ||  | ||||||||||||||||||||  ||||||| || || ||||| |||||||| || || || || |||||| ||| || ||| || |||      |  || |    || |  ||| |      | ||          ||||    | ||  |   | |  |  |||  |  
AGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTTGATTTTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaacatttat-ttggaagtttttgtgcaagtttccctaaaatgcttctgtaatttccaatacttttgaaatgaaaatcatgctttctgaattat--

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G43540.2 (Glycine max), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaattaatattgttcagatccgttctctttctcaaactaagaaagaaaagcttggcgtttttt---cttaaatgttgagtaccaaaatcctag--
||| | |||||||||||||||||||| ||  | ||||||||||| || |||||  ||||||| || || ||||| |||||||| || || || || |||||| |  ||||||   |   ||  |  ||  | ||  |   ||| |      | ||         ||||||      ||||| ||  || || |    ||   
AGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtactctgaaatttggaagtttttgtgccagtttccct---aaaatgcttctgtaatttccaatattttttaaatgaaaatgatgcttaacatatgtttatta

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaattaatattgttcagatccgttctctttctcaaactaagaaa----------gaaaagcttggcgttttttcttaaatgttgagtaccaaaatcctag
||| | ||||| ||||||||||| || ||| | || ||||||||||| ||||| |||||||| || |||||||| |||||||| |||||||| |||||||||  |  |  |  ||||| | |     |    |   ||||| | |  |  |           |||||  |     ||||   ||  |  |   |   | ||      
AGTCTTATGGAGTATGAAGAGCACGAAAAACGTGCCTGGAGTGTTGACTTTTCACGAACAGAACCATCAATGCTTGTATCTGGTAGTGACGACTGCAAGgtaaat--atctccatattttccgttatcacctttcatctcacattgggctatgtctcatataaaaagaatactacttttagatatctcctagctcttataa------

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaattaatattgttcagatccgttctctttctcaaactaagaaagaaaagcttggcgtt--ttttcttaaatgt-tgagtaccaaaatcctag
|||||||||||||| || |||||||| ||  |||||||||||||||||||||| || || || ||||||||||| ||||| || ||||| || ||||||||| |||||| || | ||   |  ||   |     ||     | ||  || | | |  ||     ||   | | ||  |||| || ||  ||        |
AGTGTGATGGAATACGAGGAGCATGAAAAGCGAGCATGGAGTGTTGATTTTTCACGCACTGAACCTTCAATGCTCGTATCCGGCAGTGATGACTGCAAGgtagttggaatttgaaatctatgggaaatggaacattgtgtgatctt-gacatatacactgaagattgactatattccatgtatgggtcacatgtgtgggg

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaa---ttaatattgttcagatccgttctctttctcaaact-aagaaagaaaagct-tggcgttttttcttaaatgttgagtaccaaaatcctag
|||||||||||||||||||||||||| ||| | |||||||||||||||||||| || ||||| || |||| ||| |||||||| ||||| ||||| ||||||||    ||   ||| |||  || | | |   ||| | |      || |||  |   ||| |     ||||  |    ||  | ||  |   ||||     
AGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGgtattgcagaacacttagtatactttaaaccaaatctatcttgattgcttaagtgatctaagataccatgtttaattgctaaaatagaaaaatgaaatgg---

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S264_64V6.1 (Physcomitrella patens), 5'ss of exon 10
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaaattaatattgttcagatccgttctctttctcaaactaagaaagaaaagcttggcgttttttcttaaatgttgagtaccaaaatcctag-----------------------------------------------------------
|| || |||||||||||||| || |||||| | || |||||||| |||||||| ||||| || ||  | ||||| || || || ||||| ||  |||||||   ||  | || |  |      |||| || | ||      |   |      |   ||||||  |     ||||| |      |         ||                                                             
AGCGTCATGGAATATGAAGAACACGAGAAACGGGCCTGGAGTGTAGATTTTTCACGAACTGACCCGACTATGCTTGTGTCAGGAAGTGATGACGGCAAGgtgaatg--atttgaagtcacgt-gatctgtcccctcaaatgataaacctgttactggcttggtttcacagcttaagtaaccgtttttggctgtctgcatttagaatgaaatccattgttcgatccattcctaggtttcttatatcgttgtatacag

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtat----ttggaa-------------attaatattgt--tcagatccgttctctttctcaaact-----aagaaagaaaagcttggcgttttttcttaaatgttgagtaccaaa---atcctag------------------------
||  | ||||||||||| |||||||| || || || |||||||| |||||||| ||||| || ||  | |||||||| || || ||||| ||| ||||||||     ||| ||             || | | ||||  |     | ||||| ||| |||| ||     ||           |||| |||||       ||||| | ||        |||| |                         
AGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAGgtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgtttttatgttactgtttgcag

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgt--atttggaaattaatattgttcagatccgttc---tctttctcaaactaagaaagaaaagcttggcgtttttt-cttaaatgttgagtaccaaaatcctag
||||| ||||| ||||| ||||| |||||  | || ||||||||||| ||||| || || || ||||||||||| || ||||| ||||| ||| |||||||   | |     |   | |  | |   || |||    | |   | |    | |        | | | |||   |  |||| | | || ||   ||  |     
AGTGTCATGGAGTATGAGGAGCACGAGAAGCGTGCCTGGAGTGTTGACTTTTCCCGGACGGATCCTTCAATGCTGGTCTCTGGAAGTGATGATGGCAAGgtctgtctcatggtctttttcttgcctttctgttgaaatatggtttagtggatgtctactttgatcgccgtccatagcttagaagctg-gtgataaggttt---

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtat----ttgg--aaattaata-ttgttcagatccgt-----tctctttctcaaactaagaaagaaaagcttggcgttttttcttaaatgttgagtaccaaaatcctag----------------
||||||||||||||||| || ||||| ||  | || |||||  | ||||||||||| ||||| || |||||||| || ||||| ||||||||| | |||||      || |  ||     ||  |||   || || |     | |  | ||  |    |      |||  || | | |  ||    | | |  | ||     ||    |                
AGTGTGATGGAATATGAGGAACATGAAAAGCGTGCTTGGAGCATCGATTTTTCTCGTACAGATCCATCAATGCTGGTTTCTGGAAGTGACGATGGAAAGgtgcagccttagttaagcccttagctgtgatgaaccatagaggtttaatgctgtagtatactttataaacttttgggctggttaccgactctgcaataatgggattactgcgttgacacattgcag

upper sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 5'ss of exon 9
AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgt-atttg--gaaat-------taatattgttcagat--ccgttc--tctttctcaaactaagaaagaaaagcttggcgttttttcttaaatgttgagtaccaaaatcctag----------------------------------------------
||  | | ||| |||||||||||||| || || ||||||||||| |||||||| ||||| || ||  | ||| |||| || || || || ||| ||||||| |||||  |||||       |  |||   |||  |  | | |    |||  |   || | |      || || |  | |  || ||     ||  | | |||    | |                                               
AGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAGgtgatttgttgaaatgttgtgattttatcactcaagtaactgatggaccttcgtttgacaaggccccttaaactggaaggtagtttttgggc-ttctgcatcaaggatcgaagcgaatgtgtagttgatcctgaagctttttgcattgtttcttgcag

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|71448214|gb|DR829264.1|DR829264
EST:     TTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAG                         GTGGGTGGATATATCAGACAACTCACTGCAGAAATGATAGTAGTTTCAGAT
genomic: TTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaa ... aaaatcctagGTGGGTGGATATATCAGACAACTCACTGCAGAAATGATAGTAGTTTCAGAT




















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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 4

AGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAGgtatttggaa ... aaaatcctagGTGGGTGGATATATCAGACAACTCACTGCAGAAATGATAGTAGTTTCAGATGGTCACAGTGATTCATGAATGCAACAACAGGTTTTTGGT




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