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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaaacaa...

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaaccaccag-aattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaaacaa
||||||||| ||  ||||||||||||||||||||||||| ||||| ||||| |||||| |||| ||||||||||||||||||||||| ||||||||||||||| |  | |  | ||    |  ||        ||||  ||  || |   |  ||     |  || ||||| |||  | | |  |    |  |    | | 
TTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCATCACGACTCTGTGTTGAAGAGgtatgttctactttattcaaataaagtcttgttaccaataaaaatataacatgtttagatctgttcctttttttcctctcaaggctaagaacgttgtaga-

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagt---aagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaa--acaa
 |||||||| ||| | || |||||||||||||| |||||||||||||| |||   || || ||| |||||||||||||||||||||| |||||||| |||||| ||  | |||     ||       |  |      | |||  ||   ||||      | |  ||||      ||  ||   |    |   |        ||||
ATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCATCACGACTGTGTGTTGATGAGgtatgcttctaatgtgttgtcttgttgatttttttttcaagagctaaaggtta-----catatgtttaaaaggatttcccgaaatagtttgggtagtggttacaa

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaata-atcagtaagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaa--acaa
 |||||||| ||| |||| |||||||||||||| |||||||||||||| |||   || || ||| |||| ||||||||||||||| | |||||||| |||||| ||  | |||   |   | |            | |||  |||   | |  ||  | |  |||     | || |||   |    |   |        ||||
ATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCATCACGATTGTGTGTTGATGAGgtatgcttctaatgtgttgttgatttttcttttttcaagagctat---taatgttacagatgtttgaaagtattgtccaaaatagtttgggtagtggttacaa

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctaccc--ctcaagagacaaacaa-
||||||||| ||| | |||||||||||||||||||||||||| ||||||||||  || || ||  |||| || || ||| |||||||||||||||| |||||  | ||    || |  ||    |  | |||        |  |    | | ||  | |    ||   |||   | |   |     || || ||  ||| |  
TTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAGCACGACTATGTGTTGATGAGgtgtgtccatgttagt--gtttatagcttaactggtgttgtcttcctcttg-tttgagatgcgtagcattgaaattcagaaatttactaaatagtgaaatatt

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaac-caccagaattatgtgttagc--ttctacacatt-tacttttgttctcccctacccctcaagagacaaacaa
||||||||| ||| | |||||||||||||||||||||||||| || ||||| || || || ||  |||| || || ||  |||| || |||||||| |||||  ||        ||   |    |  || |  ||  || |||   | ||||   ||     |||| |    | | | |  | |  | | |   |         
TTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGGCACGCCTTTGTGTTGATGAGgtgtgcttgtttacatgtttttttaggtacatgcagtaggattgaattttagaaatttactgcattgtgaactggctatggcttgtctcactttaattct----

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccc-caaataatcagtaagaaaataaaccaccagaattatgtgtta-gcttctacacatttacttttgttctcccctacccctcaagagacaaacaa
||||||||| ||| | ||||||||||| ||||| || || ||  |||||||||| || |||||  |||| || ||||||||||| || |||||||| ||||||  |     | |   ||||   |   | ||      | |  | |   |    | || ||   ||  |||| || |    || |  |  |||         
TTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCATCACGCCTTTGTGTTGATGAGgtaaccatatcactctccagttgaatgttcaagtttatgcaccagggactgtagtcctgcattgtttattttattttattttatctttttagactttttg--

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaa-----ataatcagtaagaaaataaaccaccagaattatgtgttagctt----ctacacatttacttttgttctcccctacccctcaagagacaaacaa
||||||||||||| | |||||||| |||||||| |||||||| |||||||||   ||  ||||  | ||||| ||||||||||| || |||||||| |||||| |    |      ||||    | ||         |    |||  |||  || |  |     | |  | || |||| | | |  |  |  | |              
TTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCATCACGGCTTTGTGTTGATGAGgtaaggataattattcataacttctgagtttccccttcttttgaagaatggatttgaatagccttgcggagttgctttcgatatttcagatgctttgctg---------

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ33653 (Selaginella moellendorffii), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaaacaa
 ||||||||||||||| | ||||||||||||||| || ||    |  ||  || ||  || ||| | || || || ||   |   |  || ||||| |||||  |    |  ||     || |  || | ||  |  |  |||  | | ||                                                 
GTATCAACCATATTTGCTCTCTCCAGAGAAAGGGCTGCGAGAGCTTGTACGAAGAGCTCTCGAACTTGCTAAAGATCCTGGAAAGCATTGCGTTGACGAGgtttgaaatag-tagcgcttaggtgaacagacttcacgttttaattttcag-------------------------------------------------

upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ37003 (Selaginella moellendorffii), 5'ss of exon 10
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaaacaa
 ||||||||||||||| | ||||||||||||||| || ||    |  ||  || ||  || ||| | || || || ||   |   |  |||||||| |||||  |    ||||| | ||     |  | |||   |    | | || |||  ||  |                                           
GTATCAACCATATTTGCTCTCTCCAGAGAAAGGGCTGCGAGAGCTTGTACGAAGAGCTCTCGAACTTGCTAAAGATCCTGGAAAGCATTGTGTTGACGAGgtttg----aaata-ttagcgcttaggtgaacagact---tcacgttttaattttcag------------------------------------------

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|211286766|gb|FK982432.1|FK982432
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|9254689|gb|BE345157.1|BE345157
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|211286763|gb|FK982429.1|FK982429
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCG
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|87155357|gb|DY400146.1|DY400146
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|30306992|gb|CD001665.1|CD001665
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|26557231|gb|CA829466.1|CA829466
EST:     AATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAAG                         GT-CATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACC
genomic: AATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGA-Ggtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACC
EST: gi|22472855|gb|BU037335.1|BU037335
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGGGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|211132359|gb|FK982426.1|FK982426
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
EST: gi|31361304|gb|CD445661.1|CD445661
EST:     AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAG                         GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA
genomic: AAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCA

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: 307

TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 334

TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 391

TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgcccca ... attcaattagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCATCACGACTATGTGTTGAAGAGgtacgccccaaataatcagtaagaaaataaaccaccagaattatgtgttagcttctacacatttacttttgttctcccctacccctcaagagacaaacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagacaaa