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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

Basic information

species Zea mays
transcript GRMZM2G181359_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
gtatatatatggctgtgaa--tctgtaaatattatcccagtcttttcat-----gtacgtgtgttc----aacatatttctgaaatgaa-----ttcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
|||| |  |    ||||||       ||  | |   | | | | | ||      || | | ||||     | ||| |||||||||  ||     ||    |    |||||||||||||| |||||||| |||||||| ||||| ||||| |||||||||||||| |||||||| || ||||||||||| || || || |||||||| |
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaa-catatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
||| ||| ||      |   ||   |   ||    |  | ||| |||| |      ||||| ||| |  || ||||   ||  ||| | ||||||||| || |||||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| ||||||||||| |
gtaaatacataag-acgtgccttctagcttttgatcgttgtttccatgaa-----attcaatcatttgactaaaat---tttatctcttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtac-gtgtgttcaacat-atttc--tgaaatgaattcttctatggt--agATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
   |    ||||||  ||   || |  | || |   | | ||||         | |     |||| |||||   ||| | || | || | |  |  |||||||||| |||||||| || |||||||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || || || || |||||||| |
--gtgagaatggctaaga---tgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatatt-atcccagtcttttcat-gtacgtgtgttcaacatatttctgaaatgaattct-tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
     |  ||||||  ||  |      |||| ||   |   ||||| | ||     ||       |   |||||    ||||   | |    |||||||||||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| || |||||||| |
----gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
---gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
     ||  | | | ||     |||     | || |  || | ||| |||| |  |   |    ||| |  || ||||   ||  ||  |  |||||||| || |||||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| ||||||||||| |
gtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaat----catttgactaaaat---tttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatatt-atcccagtcttttcat-gtacgtgtgttcaacatatttctgaaatgaattct-tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC------------------
     |  ||||||  ||  |      |||| ||   |   ||||| | ||     ||       |   |||||    ||||   | |    |||||||||||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| || |||||||| |                  
----gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtg-tgttcaacatatt-tctga--aatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
||  | |    ||      | |  |  |  | | |   | ||||  ||| | || |  |    ||||| || ||    |   || || |   | ||||||| ||||| || |||||||| ||||| || || |||||||| ||||| || || ||||| |||||||||||||| || ||||| ||||||||||| |
gt-cacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatattatc-ccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttc--------tatg-gtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
||   ||  |   |||  || |||  | || | |   ||| ||    || |||| | || |  ||  |  ||     |  | | |        | || | ||||||| || |||||||| || ||||||||||| || ||||| || ||||||||||| |||||||| ||||| |||||  |||| || || |||||||| |
gtgc-taatttattgtttatttgtttagatgaacattagttttcatgtg-acgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
            | | ||       |  ||    |   ||||  |   | ||  |    | | | |  |      |||| |  |  ||| |  |     | |||||||||| |||||||||||||||||||| || || ||||| || ||||| ||||| ||||||||||| || |||||| |||| || || || ||||| |
ccgccagtgtattgtttactcaaacgctaagtactgtgtattcacgtggcctacttcgatgcttatcgtggtgcgatttgtttatggaacttgtg---agcagATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatattatccca-gtcttttcatgtacgtgtgttcaaca---tatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
                      |||  |   || |   || | ||| ||   |||   | || |   | ||| |    |   |  || | |   |||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| |||||||||||  | || || || ||  | ||||||||||| || ||||
----------------------gtatgttacattctgtgtttattcctggcagtggtcttaaaagttttttttttccctttctctttttctttcagATGGCCCGATCAAAGAAAGCTTGCATTGTTTTCTTTGACGAAGTCGATGCCATTGGTGGTGCCAGATTCGACGACGGCATTGGTGGCGACAACGAAGTGC

upper sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 7
gtatatatatggctgtgaatctgtaaatattatcc-cagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
     ||| |  |    | || ||   ||||     ||||  | | |        | ||  |  | ||| |    |   || |||| |   |||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| |||||||||||  | || || || ||  | ||||||||||| || ||||
----gtatgttac----attccgtgtttattcctggcagtggtcttaaa-----attttttatttttttttcctttctctttttcttt--cagATGGCCCGATCAAAGAAAGCTTGCATTGTTTTCTTTGACGAAGTCGATGCCATTGGTGGTGCCAGATTCGACGACGGCATTGGTGGCGACAACGAAGTGC

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|67019132|gb|CO447881.1|CO447881
EST:     TGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|148930441|gb|EE284947.2|EE284947
EST:     TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|31363534|gb|CD447891.1|CD447891
EST:     TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|6031320|gb|AW076177.1|AW076177
EST:     TTCAGAAGTATGTAGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|32843790|gb|CD983471.1|CD983471
EST:     TTCAGAAGTATGTAGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTCGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|67020716|gb|CO449465.1|CO449465
EST:     TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|211115113|gb|FL138970.1|FL138970
EST:     TTCAGAAGTGTCTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|40334078|gb|CK368148.1|CK368148
EST:     GGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: GGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|32846351|gb|CD986032.1|CD986032
EST:     TTCAGAAGTATGTAGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: TTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
EST: gi|60347007|gb|DN213980.1|DN213980
EST:     AGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAG                         ATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT
genomic: AGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCT

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: 43 (upstream exon), 49 (downstream exon)
Score: 621

AGCAAATCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGTTAGTTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 642

AGCAAATCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGTTAGTTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 522

AGCAAATCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGTTAGTTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 586

AGCAAATCGGACTGATGCTTGTTTCATCCGTGTAATTGGAAGTGAGTTAGTTCAGAAGTATGTCGGCGAAGGTGCTCGGATGGTCAGGGAACTTTTCCAGgtatatatat ... tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
                                         ttcttctat  CT-rich tract
                      aacatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG