Sequence
atgc intronic sequence ATGC exonic sequence...gtacaaatagctcataattttattgaaattttttgttgattagttgcatagtttccaaattcaggcaataagtgtttaagatttaatacttgagtatcagATTCCTGGAATTTGATGAACATCCGATTGCTGCTGCATCAATTGCTCAGGTTCATCGAGGTCGGTTGAATAATAATCAGGAAGTAGCTGTGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g34830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g34830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G040720_T06 (Zea mays), 3'ss of exon 4
-gtacaaatagctcataattttattga--aattttttgttgattagttgcatagtttccaaattcaggcaataagtgtttaagatttaatacttgagtatcagATTCCTGGAATTTGATGAACATCCGATTGCTGCTGCATCAATTGCTCAGGTTCATCGAGGTCGGTTGAATAATAATCAGGAAGTAGCTGTGAAG
|||| | | | | || | | | | | | | ||| | ||||| | | | | || || | || |||||| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||| |||| ||||| || |||||||| |||
cgtactt-ttgtttgtttttctgtgggttaggtgctatataattctgtttatagtaccttatattgtgaaaaaaacat--aaatgttaatatgtgagtatcagATTCCTGGAATTTGACGAACATCCGATTGCTGCTGCATCAATTGCTCAGGTTCATCGAGGTCGATTGCATAACAATCAAGATGTAGCTGTCAAG
upper sequence: LOC_Os11g34830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G040720_T02 (Zea mays), 3'ss of exon 3
gtacaaatagctcataattttattgaaattttttgttgattagttgcatagtttccaaattcaggcaataagtgtttaagatttaatacttgagtatcagATTCCTGGAATTTGATGAACATCCGATTGCTGCTGCATCAATTGCTCAGGTTCATCGAGGTCGGTTGAATAATAATCAGGAAGTAGCTGTGAAG
||||| | | | | || || | || |||||| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||| |||| ||||| || |||||||| |||
-----------------------------------------------atagtaccttatattgtgaaaaaaacat--aaatgttaatatgtgagtatcagattcctggaatttgacgaacatccgattgctgctgcatcaattgctcagGTTCATCGAGGTCGATTGCATAACAATCAAGATGTAGCTGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatagtttccaaattcaggcaataagtgtttaagatttaatacttgagtatcagATTCCTGGAATTTGATGAACATCCGATTGCTGCTGCATCAATTGCTCAGGTTCATCGAGGTCGGTTGAATAATAATCAGGAAGTAGCTGTGAAG
atttaat putative branch site (score: 4)
aataagtgtttaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaatagctcataattttattgaaattttttgttgattagttgcatagtttccaaattcaggcaataagtgtttaagatttaatacttgagtatcagATTCCTGGAATTTGATGAACATCCGATTGCTGCTGCATCAATTGCTCAGGTTCATCGAGGTCGGTTGAATAATAATCAGGAAGTAGCTGTGAAG
gtacaaa
- - - - - - - - - - - - - - - - ttgttga
- - - - - - - - - - - - - - - - - - - - - -ttgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggcaa