Sequence
atgc intronic sequence ATGC exonic sequence...tttctgcataatcttgcatgtgctcttcgactgattagtcgaaactcgaaagtggacttgtatcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g33830.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G082174_T02 (Zea mays), 3'ss of exon 2
tttctgcataatc-ttgcatgtgctcttcgactgattagtc-gaaactcgaaagtggacttgt--atcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
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--tccatctgtttgttgcttg-accttgcgccttgttattctgccatttggttgaggatagattaatcctcaa-ttgtctgacaattgttcacgtctaatttagGTTTTTTCGGCATTTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G082174_T06 (Zea mays), 3'ss of exon 1
--------------------------------------------------tttctgcataatc-ttgcatgtgctcttcgactgattagtc-gaaactcgaaagtggacttgt--atcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
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gtacagtagctaccttgttaattcatgcctccagcatgattctccgttgtgctccatctgtttgttgcttg-accttgcgccttgttattctgccatttggttgaggatagattaatcctcaa-ttgtctgacaattgttcacgtctaatttagGTTTTTTCGGCATTTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 2
tttctgcataatcttgcatgtgctcttcgactgattagtc-gaaactcgaaagtggacttgt--atcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
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-tcccatctgttctttcct-taccttgcaccttgttattctgcgatttggttggggataggctaatcctcaa-ttgtctgtcaattgttcatgcctaatttagGTATTTTCGGCATTTGGATTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G01150.1 (Arabidopsis thaliana), 3'ss of exon 2
tttctgcataatcttgcatgtgctcttcgactgattag---tcgaaactcgaaagtggact--tgtatcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
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---atccgggaacatttgagtttctttctgttgatttggttccctaggttgttctccctccaatgtatggtcatgattaatatcga--gtccaaacttgtttcagGTATTTTCTGCTTTTGGATTTGTGCATAAAATTGCCACATTTGAGAAAGCTGCTGGTTTCCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ11787 (Selaginella moellendorffii), 3'ss of exon 2
----tttctgcat--aatcttgcat-gtgct--cttcgactgattagtcgaaactcgaaagtggacttgtatcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
|| |||||| | | ||| || ||| ||| | ||| || | | ||| || |||| | | | | | | || || ||| | |||||||||| ||||| || |||||||| ||||||||||| |||||||| |||||||||| |||
tgatttcctgcatgtagttttgaattgtggctgctttggctggtttggacgagctcttgag---acttctgttcctaaaaacgtttactttgatt---gaacgc---agGTATTTTCAGCATTCGGATTTGTCCATAAGATAGCAACGTTTGAGAAAACTGCTGGTTTTCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22628 (Selaginella moellendorffii), 3'ss of exon 2
----tttctgcat--aatcttgcat-gtgct--cttcgactgattagtcgaaactcgaaagtggacttgtatcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
|| |||||| | | ||| || ||| ||| | ||| || | | ||| || |||| | | || | | | | || || ||| | |||||||||| ||||| || |||||||| ||||||||||| |||||||| |||||||||| |||
tgatttcctgcatgtagttttgaattgtggctgctttggctggtttggacgagctcttgag---acttctgttcttaaaaatgtttactttgatt---gaacgc---agGTATTTTCAGCATTCGGATTTGTCCATAAGATAGCAACGTTTGAGAAAACTGCTGGTTTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgaaagtggacttgtatcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
aatgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctgcataatcttgcatgtgctcttcgactgattagtcgaaactcgaaagtggacttgtatcctcatcttttgtcgcaatggtttgtgaatgttttagGTATTTTCCGCATTTGGGTTTGTCCACAAGATAGCAACCTTTGAGAAGGCTGCTGGTTTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT