Sequence
atgc intronic sequence ATGC exonic sequence...tgggtgtcccagttgctgcaaatgtttgattggtttggtttcctttgttagtgacattttctggatgcttagctacagacaacgtttgctgtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 3
tgggtgtcccagttgctgcaaatgtttgattggtttggtttcctttgttag-tgacattttctggatgcttagctacagacaa--cgtttgctgtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAG
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aagatttctcatct-ttgtat-tatcacatcctgcctcttgtagttatcatctaaagcttgctatat-cttagtcaaacactgttcgtattttgtgctattagGAATCAATGGAGAAGGCTGTAAAGAACAAAGTGGCCAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAGGCACTTAG
upper sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 3
-------tgggtgtcccagttgctgcaaatgtttgattggtttggtttcctttgttagtgacattttctggatgcttagctacagacaacgt-ttgctgtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAG
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acttgcatgtctgttttaatcccatgttctctcttataactatgtatagcatggtaaatgatatc------atgctcaa--gaaaactacatattgttgtggcatcagGAAGCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTAAG
upper sequence: Vv10s0116g00490.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G070126_T01 (Zea mays), 3'ss of exon 3
tgggtgtcccagttgctgcaaatgtttgattggtttggtttcctttgttagtgacattttctggatgcttagctacagacaacgtttgctgtg--actgt-agGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAG
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aaaacgtat-agttgc-acacctgtttaaatcccatg-tgccctcttataattgtatagcatggtaacatgctcaagaaaactgcatgttgttctcctgtcagGAATCTATGGAGAAGGCTGTGAAGAACAAAGTGGCTAAAGCAGTTGTACCTGCTATTGATGTGATGTTTCAAGCACTCAGMapped 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|34549765|gb|CF517997.1|CF517997EST: AGGCGGTGTTTATGCTTTGGGTGGAGTTGGAGGCCGTGGATGTTTTTCTG GATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCT
genomic: AGGCGGTGTTTATGCTTTGGGTGGAGTTGGAGGCCGTGGATGTTTTTCTGgtacattttc ... gtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCT
EST:
gi|34550714|gb|CF518932.1|CF518932EST: AGGCGGTGTTTATGCTTTGGGTGGAGTTGGAGGCCGTGGATGTTTTTCTG GATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCT
genomic: AGGCGGTGTTTATGCTTTGGGTGGAGTTGGAGGCCGTGGATGTTTTTCTGgtacattttc ... gtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttagtgacattttctggatgcttagctacagacaacgtttgctgtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAG
acatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggtgtcccagttgctgcaaatgtttgattggtttggtttcctttgttagtgacattttctggatgcttagctacagacaacgtttgctgtgactgtagGATGCCATGGAGAAAGCAATTAAAAACAAAGTTGCCAAAGCAGTTGTACCTGCCATTGATGTTATGTTCCAAGCCCTAAG
- - tgtccca
- - - - - - - -ctgcaaa
- - - - - - - - - - - - - tgattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agacaac