Sequence
atgc intronic sequence ATGC exonic sequencegttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g06840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G132866_T01 (Zea mays), 3'ss of exon 4
gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
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-------------------------------------------------------------------------------------gttctagtactaaaatatactcatacatgccatccatgg----------atagct-aataatatactatttcaaat-cagGTGAAAAGAGGAAAAAGCTTGAAGAAGAGAAGGGGATCATTATTCGGTTCGTCATTGGCCACAG
upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 4
gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
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-------------------------------------------------------------------------------gtttttattacacttttatctttgatcaactatgttccttgatggttgtatctgattgaaatgttgttgtttt----------cagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 4
gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
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-----------------------------gttcat--ggatgtttctttgctttctattcc-------tggagttcttttttcttattcatatctt------attttagcttcttattggatgatgtcttacgattgtttcttctgg--aacacatggaaaatagGTGAAAAAAGGAAGAAGCTGGAGGAAGAGAAGGGCATTATCATTCGCTTTGTCATTGGTCATAG
upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 4
gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
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-------------------------------------------------------------------gttctgaat--tgatcctatactctttccactattttttttttttttccctgt-ttgtgaaactaatttatgacaatctttttctttatgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTGTAATAGGTCACAGMapped 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|33796729|gb|CF324232.1|CF324232EST: TAGCAGTCGGAAGAGAAGAGATTCCATACGTTACACCTGGATGCCTCAAG GTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCG
genomic: TAGCAGTCGGAAGAGAAGAGATTCCATACGTTACACCTGGATGCCTCAAGgttgttgaca ... caaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCG
EST:
gi|29657303|gb|CB653578.1|CB653578EST: TAGCAGTCGGAAGAGAAGAGATTCCATACGTTACACCTGGATGCCTCAAG GTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCG
genomic: TAGCAGTCGGAAGAGAAGAGATTCCATACGTTACACCTGGATGCCTCAAGgttgttgaca ... caaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
aactaac putative branch site (score: 1)
ttctatagttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA