Sequence
atgc intronic sequence ATGC exonic sequencegttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g22020.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G159119_T01 (Zea mays), 3'ss of exon 2
---------gttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcc-----tatatcaacaaacagtactgattaatctcgcttgtactagtt---aattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
|| | | || | | || | | | | | ||| | | | | | || || || | || |||||||| | | | | | | | | | || | | | ||||||| ||||||||||||||||| |||||||| ||||| || || ||||||||||||||||||||||||||||||||||||
gtttgttgccttgctcacccttatccattcctaccaccccatcacagaaaacttgtgtcgctgtgtacgattagtctaattaataataacaattaatctaaccaattgtgatctgaagatgctaacgtatgcg-catacattcatgcagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
upper sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G016370_T01 (Zea mays), 3'ss of exon 2
---------------------gttagtgccattttttc-tcagtgacagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
| | ||| | || ||| || | || | || |||| || ||| ||||| | | | || | | | |||| | | | | | | || | | | ||||||| |||||||||||||||||||||||||| ||||| || || ||||||||||||||||||||||||||||||||||||
gtttgttgccttgctcacccttatcctaccacctcctcatcacagaaaacttgtgtggctgtgtacgattagtctagttaataataacaatta--attaatctaac-caattgtgatgtgaagatgctaacgtatgcg-catacattcatgcagTGGCGACGCCCAAGCAGATCCGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
upper sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G21900.1 (Glycine max), 3'ss of exon 3
gttagtgccattttttctcagtga-cagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
|||| | || ||| || | | | || || | | || | ||| ||||| || || | | | || || | | || || || ||||| || |||||| |||||||||||||||| |||||||| ||||| || || ||||| || ||||| |||
--------------------gtgagtatcttagttaatttgcacaagttgctatgtgctctaa-attatgcaattgaaattggaaccgctt---tgtgtcaaatgtttgatgtttggtatttggtgtttgtagCTGCCACGCCTAAACAGATCAGGGAGCTGATGAAGGTTGATGGCCTAACCAATGATGAAGTCAAAAGTCATTTACAG
upper sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G32770.2 (Glycine max), 3'ss of exon 3
gttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccg-tgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
|| ||| | | | ||| || | || || | ||| ||| || | | || || || | | | ||||| ||||| | | || | | | || || | ||| || || || ||||| ||| | ||||||||||| || ||||||||||| || || || ||||| ||||||||||||
gtgagtatc-tcaatatatagtatgttctttttttggtaat---gatgaatatatagtatgtc--ctgattgttgtgtttga----gatgttacta--taattgcttattgataattttggctgtttctacagCTGCCACACCAAAGCAAATCAGAGAGCTGATGAATGTTGATGGCCTCACAAATGATGAAGTCAAAAGCCATTTGCAG
upper sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S166_107V6.1 (Physcomitrella patens), 3'ss of exon 5
gttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
||| | | |||| | | | | || || | |||| | | | | | ||||| ||||||||| | | ||| | ||| | | | |||| | |||| || || ||||| |||||||| ||| ||||||| |||||||||||||| |||||||| || ||||| ||| |||||
gtttctacatacttttgttggacaaaaatc-actgtacaagttga-taggaatttgacatatctgttttcagtactgaa-gttgtaagttgaa--gaacaatggatcctgacgcattttcgtgttgtaacagTTGCAACACCCAAACAGATCCGCGAGTTGATGAAAGTGGATGGCCTCACGAACGACGAAGTGAAGAGTCATCTGCAG
upper sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S83_100V6.1 (Physcomitrella patens), 3'ss of exon 4
gttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
|||||| ||| | || | | || |||| | | | | || | || | || | || | | || | | | ||| || |||||| || ||||| ||||| || || |||||||||||||| || ||||| ||||||||||| || ||||||||| |||||
-------------tttctctgtgtcggc-----------attctccttgcattttgtt-------ctggtgtttatgttggattcgaacttcacaaattcaacttca-ctgacacgggctgtggttgtgcagTTGCCACGCCAAAGCAAATACGCGAGCTGATGAAGGTCGACGGCCTTACCAACGACGAAGTGAAGAGCCATCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
tagttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcctatatcaacaaacagtactgattaatctcgcttgtactagttaattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA