Sequence
atgc intronic sequence ATGC exonic sequencegtgcatgcccgttttgcatacgtgattacctttggataattgcacatccagtaatctgatttttctaccctgttctgataatagGATCGAACCAGATAATTGCGCAGTATTACCAGCTCATTCGTCTCGGATTCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g37460.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g37460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101069_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------gtgcatgcccgttttgca-tacgtgattacctttggataattgcacatccagtaatctgatttttctaccctgttctgataatagGATCGAACCAGATAATTGCGCAGTATTACCAGCTCATTCGTCTCGGATTCGAG
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gtacggtaactctagctgttgttcctgtctgatggatttgttcgcagattatatttccactgagcaaacaaattacagtgacttcatcttctctg-ccttccttctctcttttggacgacatacagGTTCCAGCCAGATTATCGCGCAGTATTACCAGCTCATCCGCCTCGGATTCGAG
upper sequence: LOC_Os04g37460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ36644 (Selaginella moellendorffii), 3'ss of exon 5
gtgcatgcccgttttgcatacgtgattacctttggataattgcacatccagtaatctgatttttctaccctgttctgataatagGATCGAACCAGATAATTGCGCAGTATTACCAGCTCATTCGTCTCGGATTCGAG
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--------------------------gttctttgagtgttcttttgttctatcactctcttaccattctctctttt-accacagGTGCTAGTCAGATTATAGCTCAGTATTACCAGCTCATTCGTCTCGGCTTCAGG
upper sequence: LOC_Os04g37460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 5
gtgcatgcccgttttgcatacgtgattacctttggataattgcacatccagtaatctgatttttctaccctgt-tctgataatagGATCGAACCAGATAATTGCGCAGTATTACCAGCTCATTCGTCTCGGATTCGAG
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--------------------------gttctttgagtgttcttttgttctatcactc--tcttatcattctgtcttttaccacagGTGCTAGTCAGATTATAGCTCAGTATTACCAGCTCATTCGTCTCGGCTTCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttggataattgcacatccagtaatctgatttttctaccctgttctgataatagGATCGAACCAGATAATTGCGCAGTATTACCAGCTCATTCGTCTCGGATTCGAG
ttctgat putative branch site (score: 3)
tttttctaccctgttc CT-rich tract
atttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcatgcccgttttgcatacgtgattacctttggataattgcacatccagtaatctgatttttctaccctgttctgataatagGATCGAACCAGATAATTGCGCAGTATTACCAGCTCATTCGTCTCGGATTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA