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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttaagacatgcctagctgtatgttttgctgcaatcttgtgccctaccctacttcataagccatatatgctgagcttacttttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA

Basic information

species Zea mays
transcript GRMZM2G092129_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092129_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g22640.4 (Oryza sativa), 3'ss of exon 3
tttgttaagacatgcctagctgtatgttttgctgcaatcttgtgccctaccctact---tcataagccatatatgctgagcttacttttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA
     |   |    || || | | | ||||  |  ||   ||| |  |    |  |   |  ||   | | |  |     || |  ||| | ||  |||| ||||||| || | ||| || |||||||| ||||| ||||||||||||||||| || |||||||||||||||||| |||||||||||||||| ||||||||||
---aatctcattctccaagttattttttttcttaaaagtatgtactatgttttggtagattttagttcttctgggggctactaaacttttagttccatttcagGCTGCCACTGCAGTAGTCAAGGAATCTGTTGAGCCACTGCTAGATGATTATCGACCTCCAGGAATAAAATCTCTGAAGTTCAGCAAATTCTCTCTTGGAA

upper sequence: GRMZM2G092129_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G02370.2 (Glycine max), 3'ss of exon 3
tttgttaagacatgcctagctgtatgttttgctgcaatctt----gtgc---cctaccctacttca-taagccatata-tgctgagcttacttttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA
     |  || |    |  |  ||  |||   ||||| | |    |||    |||    | ||| | ||    | ||| |  |||  ||  ||||  |||   |||||||| |||||  | ||| | |  ||||| ||||||||||||||||| || ||| | ||||||||||| |  || ||||||||||||||  | || |||||||
-----ttggagaccttttacattaaatttccttgcaaacatagaggtgtattcctgttttgcttaaatagatgacataatattga--ttgattttgttttc--ttttagGCAGCAACCTTGGTGATCAGAGAATCTGTTGAACCACTGCTAGAAGAGTACAGACCTCCAGGAATTACTTCATTGAAGTTCAGCAAGCTGTCACTTGGAA

upper sequence: GRMZM2G092129_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G09070.1 (Glycine max), 3'ss of exon 4
--tttgttaagacatgcctagctgtatgttttgctgcaatcttgtgccctaccctacttcataagccatatatgctgagcttactt--ttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA
    | ||| |  |    |   || |    | |  |   | |  ||   | |   |    |||    || |    |||  ||  ||  ||   |||  |||||||| |||||  | ||| | |  ||||| ||||||||||||||||| || ||| | ||||||||||| |  || ||||||||||||||  | || |||||||
gaccttttacgttaaatttccttgcaaacatagaggtgttttcctgttttgcttaa----atagatgatgtgatttgatattgattgattttgttttcttttagGCAGCAACCATGGTGATAAGAGAATCTGTTGAACCACTGCTAGAAGAGTACAGACCTCCAGGAATTACTTCATTGAAGTTCAGCAAGCTGTCACTTGGAA

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|211162012|gb|FL219539.1|FL219539
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
EST: gi|211162016|gb|FL219543.1|FL219543
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGGAATCCGTTGAACCACTGCTAGATGATTA
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGG-AATCCGTTGAACCACTGCTAGATGATTA
EST: gi|148971559|gb|EE022272.2|EE022272
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
EST: gi|74241137|gb|DT649051.1|DT649051
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTA
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAA-CAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTA
EST: gi|71331353|gb|DR802511.1|DR802511
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
EST: gi|211162015|gb|FL219542.1|FL219542
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
EST: gi|211162018|gb|FL219545.1|FL219545
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
EST: gi|211162017|gb|FL219544.1|FL219544
EST:     TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAA                         GCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC
genomic: TTAAATGGTTGAACAAGCATCTGAGCAAACTTTGGCCTTTTGTTGTAGAAgtaagtttaa ... ttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaccctacttcataagccatatatgctgagcttacttttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA
                                           ttttaat  putative branch site (score: 3)
                                cttacttttcatttt  CT-rich tract
                                 ttacttttcattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttaagacatgcctagctgtatgttttgctgcaatcttgtgccctaccctacttcataagccatatatgctgagcttacttttcattttaattttagGCTGCAACAGTAGTGGTTAAGGAATCCGTTGAACCACTGCTAGATGATTACCGGCCTCCAGGAATAAAATCTTTGAAGTTCAGCAAATTTTCTCTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - -acatgcc
- - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - ttgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatt