Sequence
atgc intronic sequence ATGC exonic sequence...aatgtttaggaataatttgttatttccccattaaaatgccaagtccattttttttttaccttgagctacatgtgtttatacagtcttatgtgactttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g17460.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g17460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G388148_T01 (Zea mays), 3'ss of exon 3
aatgtttaggaataatttgt--tatttccccattaaaatgccaagtccattttttttttaccttgagctacatgtgtttat---acagtcttat--gtgactttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA
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cttaatccatatttgtttgtgctatttcccaaccaatacac----tctagtttctttg---cttgagctgcatgtgaccactgcactacttgactaatgtctattagGATAATTCTGGAGCAGTCCCTCTCGTAGCAAAGCACCATAAAGGTTGTCATTGCAAGAAGTCAGGATGCCTAAAGAAGTACTGTGAATGCTACCAAGCAA
upper sequence: LOC_Os02g17460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
----------------------------------------aatgtttaggaataatttgttatttcc--ccattaaaatgccaagt-ccattttttttttaccttgagctacatgtg-tttatacagtcttatgtgac-tttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA------
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gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGT-GAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
upper sequence: LOC_Os02g17460.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------aatgtttaggaat--aatttgttatttcccca-ttaaaatgccaagtccattttttttttaccttgagctaca-tgtgtttatacagtcttatgtgactttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA------
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gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaata-tcttgtttgaacacagGAATG----TGAA---ATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttttttttaccttgagctacatgtgtttatacagtcttatgtgactttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA
ctttc CT-rich tract
ttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgtttaggaataatttgttatttccccattaaaatgccaagtccattttttttttaccttgagctacatgtgtttatacagtcttatgtgactttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - -aggaataa
- - - - - - - - - - - - - - - - - - tgccaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttatg