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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattaggaatggagcatcaccgtagtcacttttagcttcctctttctaacttgcttatcaactgtggatgttgcag

Basic information

species Zea mays
transcript GRMZM2G177001_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 5'ss of exon 4
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgt-aaaatcatgttggttc-----------agattaggaatggagca-tcaccgta-gtcacttttagcttcctctttctaacttgcttat--caactgtggatgttgcag
|| |||||||||||| ||||||||||||| |||||||||||  ||||||| || || |||||||| || ||| ||||||| || || || || ||||||||| ||||||   ||   |               | ||      | || |   | ||    ||  | | ||| |||        | ||||||  ||||| ||||| ||||||
CCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTTGAGAGGTTCACAACAGACAAGCAAAGgtcaaaatctctttaccttttccccctcttgattcagatggaaaacacttgtcatatagaaccctaaactttctcagaacctttagcttattccaactatggatcttgcag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G39300.1 (Glycine max), 5'ss of exon 4
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattaggaatggagcatcaccgtagtcacttttagcttcctctttctaacttgcttatcaactgtggatgttgcag
|| || |||||  |  | | ||||||  | | | | || || || ||||||| ||||||||||||||| ||| | ||||| |||||||||||||| ||||||       ||     | |    |    |     |   |  | ||   | ||| || |    |  ||  ||  |  |   ||     ||| | ||
CCAAAGAATGTTTCTGAAGTTGAAATATCTGCTCTTTTCTCCAAGTATGGAACTATAAAGGATTTACAAATTTTAAGAGGTTCTCAGCAAACGAGTAAAGgtgctgatttgacaccttaatcaatcctttatttaaggctttggtgtttcttaactgcaaagtgtta--ttcatagttctcttactttgtggtag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G36650.2 (Glycine max), 5'ss of exon 4
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattaggaatggagcatcaccgtagtcacttttagcttcctctttctaacttgcttatcaactgtggatgttgcag
|| || |||||  |  | | ||||||  | | | | || || || ||||||| ||||||||||||||| ||| | |||||||||||||||||||| ||||||       |      | |    |    |     |   || | ||   | ||| || | |     ||  ||  |  |   ||     ||| | ||
CCAAAGAATGTTTCTGAAGTTGAAATATCTGCTCTTTTCTCCAAGTATGGAACTATAAAGGATTTACAAATTTTAAGAGGCTCTCAGCAAACGAGTAAAGgtgctgatttcacacattaatcaatcctttatttaaggccttggtgtttcttaactgcatagagtta--ttcatagttctcttattttgtggtag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G17090.1 (Glycine max), 5'ss of exon 4
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattagga-atggagcatcaccgtagtcacttttagcttcctctttctaa--cttgcttatcaactgtggatgttgcag---
|| || ||| |  |  | | |||  |  |  || | || ||||| ||||||| ||||||||||||||||||| | ||||| |||||||| || || ||||||     | |  || | ||||| | |  ||     ||  || | |    || ||||||| |  |   ||  |||  ||   | ||||     ||   |   
CCAAAGAATATTTCTGAAGATGAGGTCTCCAATCTTTTCTCAAAGTATGGAACTATAAAGGATTTACAGATTTTAAGAGGTTCTCAGCACACAAGTAAAGgtg----cctaatgttacagatgaagccattctttattccctttgagcattgtagcttcttaatagcaaagctttattcgtagctgtattcctttgtgtag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G02700.3 (Glycine max), 5'ss of exon 3
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattagga-atggagcatcaccgtagtcacttttagcttcctctttctaa--cttgcttatcaactgtggatgttgcag---
|| || ||| |  |  | | |||  |  | ||| | || ||||  ||||||| ||||||||||||||||||| | ||||| |||||||| || || ||||||     | |  || | ||||| | |  ||     ||  |  | |    || ||| ||| |  |   ||  |||  ||   | ||||     ||  ||   
CCAAAGAATATTTCTGAAGATGAGGTCTCTGATCTTTTCTCAATGTATGGAACTATAAAGGATTTACAGATTTTAAGAGGTTCTCAGCAGACAAGTAAAGgtg----cctaatgttacagatgaagctatcctttattccttttgggcattgtagtttcttaatagcaaagctttattcatagctgtattcctttgagtag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G03110.1 (Arabidopsis thaliana), 5'ss of exon 4
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattaggaatg-gagcatcaccgtagtcacttttagcttcctctttctaacttgcttatcaactgtggatgttgcag
|| || |||||  |  | |||||| |      |||||| || || || || |  ||||||||| |||||||||| |||||  |||| |||||||||||||||  |||| | |   |     |    | || || | |     |    | |||    | |||  || | || |  || |    ||| ||||||  ||
CCAAAGAATGTCTCTGAAGCTGAAGTTCAATCTTTATTCTCCAAGTACGGGACCATAAAGGATCTACAGATTCTAAGAGGTGCTCAACAAACGAGCAAAGgttgaatc-tatc--tctgtgtcgctattgtgatctttggtttcactagtttgctttacctagttttgacct-tttgtttgttgtcgatgtt-tag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 5'ss of exon 4
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttg----gttcagattaggaatggagcatc-----accgtagtcacttttagctt--cctctttctaacttgc----ttatcaactgtggatgttgcag
|| || |||||  |  | |||||| |  |   ||||||||| |||||||||| |||||| || ||||| ||||||||||| |||||||| || ||||||||||   |    |       |||   ||  |||| |   ||      ||  | || || |  | |||  | |  ||   | |||      |||  | | |   | | ||||
CCGAAGAATGTTTCTGAAGCTGAAGTTTCTTCTTTATTTTCTAAATATGGAACTATAAAAGACTTACAAATTCTGAGAGGTTCTCAGCAGACAAGCAAAGgtattgtttcataatcctattccttttgtgaattgtttatttgtagactattgtgacctcaaacttgacatggtttgtatttgtacctctatttattctatttatggcag

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|149108797|gb|EE189842.2|EE189842
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|60400937|gb|DN233744.1|DN233744
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|149098711|gb|EE184722.2|EE184722
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|71438922|gb|DR819972.1|DR819972
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|211051931|gb|FL422541.1|FL422541
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|89761503|gb|DY689493.1|DY689493
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|60396221|gb|DN229090.1|DN229090
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|6020453|gb|AW065381.1|AW065381
EST:     ATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: ATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
EST: gi|6564129|gb|AW231751.1|AW231751
EST:     AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAG                         CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA
genomic: AAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTA

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: 105

CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 42

CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 52

CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcat ... gatgttgcagCTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAAAAATGTAACACATGCTGAAATGACGGATTTATTTTCAAAATATGGAAATATAAAGGATTTACAGATTCTGAGAGGCTCTCAGCAAACGAGCAAAGgtaaaatcatgttggttcagattaggaatggagcatcaccgtagtcacttttagcttcctctttctaacttgcttatcaactgtggatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG