Sequence
atgc intronic sequence ATGC exonic sequencegttagtggttttacattaaaatcagtcatcaactattctgctcccctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40740.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 3
gttagtggttttacattaaaatcagtcatcaactattctgctcccctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
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-----aggacagacat-atattcatttctttcccatgctcatattatacttctatattgccatctagccagtttaagacattctttatt-tatctttttttttgcagGTTCTTTACAAGCATAAGATTGTTCTATTTGGTGGCTTTTATGACACTCTTAGGGAAGTGAG
upper sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 6
gttagtggttttacattaaaatcagtcatca-actattctgctcccctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
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---tgtgtgccccccccaatatcatatggcatattaatccagtttttttttgtcttcatcatatagttgttt-----gttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG
upper sequence: LOC_Os04g40740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 6
gttagtggttttacattaaaatca-gtcatcaactattctgctccc-ctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
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-------cccccccacccccatcatatggatacccatattaatccagttttttttgtcttcat-catatat-ttgtttgttctaatgctttattttggttaattaacagGTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
ccttaat putative branch site (score: 4)
ttgtgttctttttcct putative PPT
taatatttctgtatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtggttttacattaaaatcagtcatcaactattctgctcccctcttttcaccttaatatttctgtattatgagcagtagtaaattgtgttctttttcctacagGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG