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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatgaaattaagacagcaattctgtattttttttacttgagtatttttgtgagctaacttcaacaatggcag

Basic information

species Zea mays
transcript GRMZM2G028004_T05
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028004_T05 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g27850.1 (Oryza sativa), 5'ss of exon 7
GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatgaaattaagacagcaattctgt--attttttttacttgagtatt---------tttgtgagctaacttcaacaatggcag
 ||||||||||| | || ||||||| |||||| |||||| |||||||||| || ||||| ||||||||  |||||| ||  ||   |    |    |||     | || |||  ||||| ||||         |||   ||||||||||||  |   |||
TCTATAGAGAAGAGGATTTCTGTGTACTCTCAGATACCTGAAGAAAATGGAGAACTCATCCAAGTATTACGgtactagaataaccgacagtattttttcccctaagttctttgccttgattattaatcaatcattttcaagctaacttcaagtactacag

upper sequence: GRMZM2G028004_T05 (Zea mays), 5'ss of exon 7
lower sequence: Vv05s0062g01220.t01 (Vitis vinifera), 5'ss of exon 8
GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgt----acttgatgaaatta-----agacagcaattctgtattttttttacttgagtatttttgtga----gctaacttcaacaatggcag--
|| || || || |||||||| || |  |||||| | ||    ||||||||||||||||| |||||||||||||    || | |   | |||     | |   ||  ||   |        |||    | ||   || |    |||||| ||  ||   |||   
GCCATTGAAAAACGAATATCCGTCTATTCTCAAGTTCCAGTTGAAAATGGGGAGCTCATCCAAGTATTGAGgtggggacctaacttatttactggtaaaatacagctcatgaacagggagactaatatgttacagtaacaaggctaacatctgcagaagcacag
















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|24768774|gb|CA403903.1|CA403903
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|37395929|gb|CF635251.1|CF635251
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAACTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|31353632|gb|CD437989.1|CD437989
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|60357917|gb|DN224890.1|DN224890
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTTTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|24768702|gb|CA403831.1|CA403831
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|67013389|gb|CO442138.1|CO442138
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|5901353|gb|AW042453.1|AW042453
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|67013387|gb|CO442136.1|CO442136
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|31364601|gb|CD448956.1|CD448956
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|211001688|gb|FL223536.1|FL223536
EST:     GTTTCTCTCAA-TACCTAAAGAAAATGGGGAGCTCATTTCA-GTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACCC
genomic: GTT-CTCTCAAATACCTAAAGAAAATGGGGAGCTCATT-CAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|18650084|gb|BM498903.1|BM498903
EST:     AGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: AGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|60357918|gb|DN224891.1|DN224891
EST:     AAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATGGAG                         GTATGAAGGTAGTCAGTATTATAGACCACATCATGATTACTTCTTTGACAC
genomic: AAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|60355576|gb|DN222549.1|DN222549
EST:     GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
genomic: GTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC
EST: gi|31363979|gb|CD448334.1|CD448334
EST:     AAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAG                         GTATGAACCTAGTCAGTATTATAGCCCACATCATGATTACTTCTCTGACAC
genomic: AAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACAC

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: 48 (upstream exon), 48 (downstream exon)
Score: 90

GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACACT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACACT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 79

GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatg ... acaatggcagGTATGAAGCTAGTCAGTATTATAGACCACATCATGATTACTTCTCTGACACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATAGAGAAGCGAATATCTGTGTTCTCTCAAATACCTAAAGAAAATGGGGAGCTCATTCAAGTATTGAGgtacttgatgaaattaagacagcaattctgtattttttttacttgagtatttttgtgagctaacttcaacaatggcag

- - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA