Sequence
atgc intronic sequence ATGC exonic sequence...catcctgaacaacataacccccagaaaaattcagtactagtagtacatatatatagtcatataacaaatcaaaataatctgtatatgaacatgacaggagTTCCGTGGAGCGAGGAGGAGCACCGGCTGTTCCTCGTCGGGCTCGAGAAGCTGGGCAAGGGCGACTGGCGAGGCATCTCCCGGAGCTACGTCACGACGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g41900.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g41900.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G071977_T01 (Zea mays), 3'ss of exon 1
--catcctgaacaacataacccccagaaaaattcagtactagtagtacatatatatagtcatataacaaatcaaaataatctgtatatgaacatgac---aggagTTCCGTGGAGCGAGGAGGAGCACCGGCTGTTCCTCGTCGGGCTCGAGAAGCTGGGCAAGGGCGACTGGCGAGGCATCTCCCGGAGCTACGTCACGACGAG
| | || | || ||| | | || || | || | | | | || | ||| || | ||| || | || || ||||||||| |||||||||||||||||| ||| |||||| ||| || |||||||||||||||||||||||||||||||||||| |||||||||| ||||
gcaactgtaaatcaagccactgagagatatagtcggt-tgaataat-cggttggttggtaacatagcagctggtgtgtttctaagcataagcaatactgcagGAGTTCCATGGAGCGAGGAGGAGCACAGGCAGTTCCTTTCCGGCCTGGAGAAGCTGGGCAAGGGCGACTGGCGAGGCATCTCCAGGAGCTACGTGCCGAC---
upper sequence: LOC_Os01g41900.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G065829_T02 (Zea mays), 3'ss of exon 1
-----catcctgaacaacat-aacccccagaaaaattcagtactagtagtacatatatatagtcatataacaaatcaaaataatctgtatatgaacatgacaggagTTCCGTGGAGCGAGGAGGAGCACCGGCTGTTCCTCGTCGGGCTCGAGAAGCTGGGCAAGGGCGACTGGCGAGGCATCTCCCGGAGCTACGTCACGACGAG
|||| ||| || | || | || ||| || || | | || || | ||||| | || | || || | | |||||||||| |||||||||||||||||| ||| |||||| | ||| || || |||||||||||||||||||||||||||||| || |||||||||| ||||
agtgcttccctgcacattattgagtccttgttgggttggtcggtagcagctgatgtttctaaaca-aaaacaatactctg-gatatatac-cgacgacgccagGAGTTCCATGGAGCGAGGAGGAGCACAGGCAGTTCCTTGCCGGCCTGGACAAGCTGGGCAAGGGCGACTGGCGAGGCATCGCCAGGAGCTACGTGCCGAC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatatatagtcatataacaaatcaaaataatctgtatatgaacatgacaggagTTCCGTGGAGCGAGGAGGAGCACCGGCTGTTCCTCGTCGGGCTCGAGAAGCTGGGCAAGGGCGACTGGCGAGGCATCTCCCGGAGCTACGTCACGACGAG
atataac putative branch site (score: 3)
atatagtcatataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcctgaacaacataacccccagaaaaattcagtactagtagtacatatatatagtcatataacaaatcaaaataatctgtatatgaacatgacaggagTTCCGTGGAGCGAGGAGGAGCACCGGCTGTTCCTCGTCGGGCTCGAGAAGCTGGGCAAGGGCGACTGGCGAGGCATCTCCCGGAGCTACGTCACGACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- -cctgaac
- - - - - aacataac
- - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa