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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

Basic information

species Zea mays
transcript GRMZM2G063949_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
gttagtaaattagcttgttatttttgccactgt-gtagctgatggtcttcct--tctcgttttaat-tattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
                         |  | ||  ||| ||  || | ||| |    |    | ||    || |   | | |  || |||| | |  |||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||
-------------------------gtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 2
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
    || |  | |||| |  ||  |   | | | ||    ||   ||   | |  || || |   ||   |||    |   ||   |       ||||||| ||||| ||||||||| | || |||||||| ||||||||||| ||||||||||||||| | ||||| |||||||| ||  |||||||||| |||||
----gtgagct-gcttttgtttggtttaattttttattgcatatactgtttccatgtcttgaccttt---gtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
    || | ||   ||||  ||||||     |||||  || |  | || |||    |||| || ||| ||   | | | | ||        |  ||||||| ||||| ||||||||| | || |||||||| || || || || || |||||||||||  | ||||| |||||||||||  |||||||||| |||||
----gtgagttgatttgtattttttgttttggtgta--tgtt--tttttctttcaattttgataattcttactagtgtgtgatca-----tcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 4
gttag-taaattagcttgttatt-tttgccactgtgta-gctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
|| || | | || | ||| | |  |||   | || |||  ||| |    ||  |||  || || |   ||   |||    |   ||   |       ||||||| ||||| ||||||||| | || |||||||| ||||| ||||| ||||||||||||||| | ||||| |||||||| ||  ||||||| || |||||
gtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgaccttt---gtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 4
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
    || | ||    | || ||||||     |||| | |  |  | ||| || ||  |||  |||  ||| ||| |  | | | ||  ||   | |||||| ||||| ||||||||| | || |||||||| ||||| ||||| || |||||||||||  | ||||| |||||||||||  |||||||||| |||||
----gtgagttttgat-ttgtttttgtttaggtgttgtttttttttttctttttcaattttgtta--attctcactgatgtgt-gattattggc-agCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
         | ||| | || | |||   |   ||| | | |          | |    |||| |       ||| || ||| |||         ||||||| ||||| || ||||| ||||| ||||| |||||  ||||||| || ||||||||||| |||||||| ||||| || ||  ||||||||||||| ||
--------gtaagcat-ttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaact-------tcacttgtttcttg------tgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
          ||  | ||| || || |      | |  |  | || |     | |     | ||  |   |||| |||||| | |         ||||||| ||||| || ||||| || || ||||| || || ||||| ||||| ||||||||||| |||||||| ||||| |||||  ||||||||||||| ||
---------gtatgtagtt-ttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctgg------ttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA

upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
|| ||| || |      | | | | |    |   || |      |||  ||  | | | |  || | ||| |  |||| ||||| |  ||  || ||||||||||||||| |||||||| || ||||| || ||||| ||||| || |||||||| || || ||||| |||||||||||  ||||||||||||||||
gtgagtcaacttttccatcaatctggatgtttcttaacatgca-tctgtctcatagatct--ttctaattttttttttattatt-attatttac-agCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA

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|22715502|gb|BU197799.1|BU197799
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|67020065|gb|CO448814.1|CO448814
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTNGTATTTG                         CTGAAGGTGCANAANATGGCCTTGATT-CACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|109637685|gb|EC591230.1|EC591230
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|149086197|gb|EE175737.2|EE175737
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|101398997|gb|EB821371.1|EB821371
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCA
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCA
EST: gi|40337281|gb|CK371351.1|CK371351
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|60356652|gb|DN223625.1|DN223625
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|32868566|gb|CF008248.1|CF008248
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|67020590|gb|CO449339.1|CO449339
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|67011006|gb|CO439755.1|CO439755
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|31356398|gb|CD440755.1|CD440755
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|7137694|gb|AW499223.1|AW499223
EST:     GCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: GCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|31355714|gb|CD440071.1|CD440071
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
EST: gi|149098034|gb|EE183981.2|EE183981
EST:     AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTG                         CTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT
genomic: AAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 312

GTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 155

GTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

GTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 162

GTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaat ... catccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA
              ttttaat  putative branch site (score: 162)
              ttttaattattattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA