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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatcagtgatgcagacttatgtttcaattatatggtgttgatactgttggcattccatgtaagctgatcgtattaataccttttttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA

Basic information

species Zea mays
transcript GRMZM2G122135_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 7
gtgatatcagtgatgcagacttatgtttcaattatatggtgt------tgatactgttggcattccatgtaagctgatcgtattaataccttttttttg---gcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
      | | || | || ||| ||| |        || || |      |  | || |    ||| |    || ||   | | || ||   ||||| ||    ||||||||| || || || ||||||||||| |||||||||||  |  |||||||||||||||| ||||| || || || || || |||||||||||||| || |
-----tttaatgctaca-actaatgctgtggcagcattgtttaacctttttttctttcaaaatttccaagaaactatgcctgtttatgtgtttttctttattgcagGATGCAACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
-gtgatatcagtgatgcagacttatgtttcaattatatggtgttgatactgttggcattccatgtaa--gctgatcgtattaataccttttttttg--gcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
    | || |   |   | |  ||| |||| |   ||| ||  |  || |  |   |||   |||||  |   |||  | |  |||||| | ||    |||||| || || || || ||||||||||| ||||| || ||  |  |||||||||||||||| || || || || ||||| ||||||||||||||||| || |
taaaagataatcaaca-aaatctat-tttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 7
gtgatat-cagtgatgcagacttatgtttcaattatatggtgttgatactgttggcattccatgtaagctgatcgtattaataccttttttttg--gcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
 | | |   |||     | |  ||| ||  |     || ||| |   | |  |    |    |  | |   |||  | |  |||||| | ||    |||||| || || || || ||||||||||| ||||| || ||  |  |||||||||||||||| || || || || ||||| ||||||||||||||||| || |
ataaaagatagtacacaaaatctattttctaggctaattgtgatagcagtagttttttggtgtaaatgtgaatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
---gtgatatcagtgatgcagacttatgtttcaattatatggtgttgatactgttg-gcattccatgtaagctgatcgtattaataccttttttttg--gcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
    |||| |||   || || | ||||  |   | |  ||  |  || ||   |   |  |      |  | |    | | |    | |  ||  ||  ||||||||| || || || || ||||||||||||||||| ||| |  |||||||||| ||||| ||||| || || || || || ||||||||||||||  | |
caattgatctca-caattcaaatttat--tgggagtgcatttttctgttaagatcatgtttcttgaattggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgatatcagtgatgcagacttatgtttcaattatatggtgttgata---ctgttggcattccatgtaagctgatcgtat-taataccttttttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
 | | |     |||  | | || ||  ||  |  ||   | |  |||   || |    | |       |  | |  |||| |  |  | |  |||| |||||| |||||||| || || ||||| || || ||||| ||  || |||||||||||||||||||||| || || || || ||||||||||| ||||| || |
-tcaaactttggattgatatttctgcatccttcttaatatctgcataagcctctcaaaagtgatctgcatttcaatgtatcttttggcatcatttttgcagGAAGCTACCATTGAGCAACTTCTGCCCATATTTCTGTCACTGTTGAAGGATGAATTTCCAGATGTGCGACTAAATATTATCAGCAAGCTAGATCAAGTGA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgatatcagtgatgcagacttatgtt-tcaattatatggtgttgata-ctgttggcattccatgta-agctgatcgtattaataccttttttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
||  ||| | |  |  |   ||   |   ||| |   |     || || |   ||  |  | | ||  |  |    ||     |   ||| | |  |||||| ||||| || || || ||| | || || || || ||  || ||||||||||||||||||| || ||||| || || ||||||||||| ||||| || |
gttttataatttttaaaattttccatgaccaactgagtatatatgctatccaatgagagacaacgtgtaattccgtgttgctttggttttatctatgcagGAAGCTACTATTGAGCAACTTTTACCCATATTCCTATCACTGTTGAAGGATGAATTTCCAGACGTGCGGCTAAATATCATCAGCAAGCTAGATCAAGTCA

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|120480796|gb|EH211024.1|EH211024
EST:     GTTCAGCTTTAGCCTCAKTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|31356310|gb|CD440667.1|CD440667
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|211334572|gb|FL404959.1|FL404959
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|40336631|gb|CK370701.1|CK370701
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|67034361|gb|CO462911.1|CO462911
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTNAC-ATGGAACAGCTTCTTTCA-TTTTTCTCTCTTTGCTGAAGGA
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCT-ACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGA
EST: gi|32914759|gb|CF019571.1|CF019571
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|24763712|gb|CA398883.1|CA398883
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|211221964|gb|FL414368.1|FL414368
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|32919959|gb|CF024771.1|CF024771
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|32849378|gb|CD989059.1|CD989059
EST:     TACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: TACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
EST: gi|31361222|gb|CD445579.1|CD445579
EST:     GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT
genomic: GTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatactgttggcattccatgtaagctgatcgtattaataccttttttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA
                                tattaat  putative branch site (score: 2)
                                      tacctttttttt  CT-rich tract
                                tattaatacctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatatcagtgatgcagacttatgtttcaattatatggtgttgatactgttggcattccatgtaagctgatcgtattaataccttttttttggcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT