Sequence
atgc intronic sequence ATGC exonic sequence...gggggcaggtttaaaatcatatacataccttcataatggcaaaagtctgtgtcactgggcttagttactaacatctgtttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAGTTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
-gggggcaggtttaaaatcatatac-ataccttcataatggcaaaagtctgtgtcactgggcttagttactaacatctgtttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAG--TTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG
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ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgtcttttcttgtgatatctcacaagt-ttgcattgctatatttgg-acagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACAT-TAGAAGATATTC-
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 8
gggggcaggtttaaaat-catatacataccttcataatggcaaaagtctgtgtcactgggct-tagttactaacatctg-tttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAGTTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG
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-ataacatttctaatatgtctatgtattatacttctcagggactattttattttatcaagctctagaatctaacatctgacttaaattgtttccttggca--gAGATATCACCACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGATACTTGAGGCAAACTACAGCATCCATGTCAGTTTCAGTGTTCTTGACTG
upper sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 8
-gggggcaggtttaaaatca-tatacataccttcataatggcaaaagtctgtgtcactgggct-tagttactaacatctg-tttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAGTTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG
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gctatttggatttggcaccaatacgattaccttctcagggactat--tttattttatcaagctctagaatctaacatctgacttaaattgtttccttggca--gAGATATCACTACTACATTTCCCAGTTTTGTTTTTCACTCACAAGTTGATGATACTTGAGGCAAACCACAGCATCCATGTCAGTTTCAGTGTTCTTGACTGMapped 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|110380717|gb|EC946005.1|EC946005EST: GTTTTGCGACATCCATCTCTTTTGAAGAATATGACCCTTCAATACCTAAA AGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGA
genomic: GTTTTGCGACATCCATCTCTTTTGAAGAATATGACCCTTCAATACCTAAAgtaagttctc ... ttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGA
EST:
gi|77582686|gb|DV220332.1|DV220332EST: GTTTTGCGACATCCATCTCTTTTGAAGAATATGACCCTTCAATACCTAAA AGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGA
genomic: GTTTTGCGACATCCATCTCTTTTGAAGAATATGACCCTTCAATACCTAAAgtaagttctc ... ttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtgtcactgggcttagttactaacatctgtttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAGTTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG
tactaac putative branch site (score: 0)
tttcatccgtttctt putative PPT
ttagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggggcaggtttaaaatcatatacataccttcataatggcaaaagtctgtgtcactgggcttagttactaacatctgtttcatccgtttcttgaacacagAGACATCACCACTACATTCCCAAGTTTTGTGTTTCACTCACAAGTGGATGACACTTGAGTTGCAGAGCTACATCAAGTTCTATCATCTTGAACAGGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT