Sequence
atgc intronic sequence ATGC exonic sequence...ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactgacactcagacgcacgtacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g36890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
ctataggagtagtag-attcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactgacactcagacgcacg-tacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
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ccaaaccttctttactgttcgagttactagt-aacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaa-tgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
upper sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S2_60V6.1 (Physcomitrella patens), 3'ss of exon 1
ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgc--aggaaaaaaaataaaaggtaactgacactcagacgcacgtacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
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-gatatagacca-agacccagtgtgtttttatttttttattgtttaatttatttttatttgtgttggtattcatttctaaataattcttttcccaaatgtagATGGTCTGCTATAGCAAGTCATCTTCCCCGCCGCACTGACAACGAGATTAAAAACTACTGGAACACTCACTTGAAGAAGAGACTCCTGCAAATCGGAATT
upper sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
---ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactgacactcagacgcacgtacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
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tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcg-tggagcac--agaaaaattgattttttggaatgtgttgttgttgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT
upper sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S106_216V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactg-acactcagacgcacg--tacac-agGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
| | | | | | | | | | || || | | ||| | || |||| | |||| | | | | | | || || ||||| || |||||| || || || |||| || ||||||||||| |||||||||||||||||||| ||||||| | | || |||||| |||
gtactgaattttcttcccgtcgcgttgggatgtctcatttctgca-gacgtcgcgcgttggttacactccac-aaaattgtcagttcctaacagcatttctcgtttcttgattgcattagATGGTCAGCCATCGCGGGCCATCTCCCCCAGCGTACAGACAACGAGATAAAGAACTACTGGAACACGCATTTGAAGAAACGTTTGGCACAGATGGGAATC
upper sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 2
ctataggagtagtagattcaggtggtaaaag--agaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactgac-actcagacgcacgtac-acagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
| | | | || ||| | |||| || || | | | | | | || ||| | | | | | || |||||||| || || || | || || || || || ||||||||||| || |||||||||||||||||| ||| |||| | || ||||| ||
---ttgaaattttac-ttctttttgtaacagttaggactagttatcttgaataccatttttttaatatatcgctttcttatttatttatttatttatattgtagGTGGTCAGCCATAGCAAGCCATCTTCCCCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACGCACTTGAGGAAGCGACTGCTGCAAATGGGGATT
upper sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaat--aaaaggtaactgacactcagacgcacgtac-acagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
|| | | || | | | | | ||| |||||||| | | | || | | || | | | ||| ||||| || || || | || || || || || ||||||||||| || |||||||||||||| ||| |||||||| | || ||||| ||
gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcgaagttccatgtggtagccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacaatgcaggaaaaaaaataaaaggtaactgacactcagacgcacgtacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
aactgac putative branch site (score: 2)
aaaaaaaataaaaggt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctataggagtagtagattcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactgacactcagacgcacgtacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - aaaagaga
- - - - - - - - - - - - - - - - - - - -cagttgc
- - - - - - - - - - - - - - - - - - - - - - - - caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacac