Sequence
atgc intronic sequence ATGC exonic sequence...caatcacagattaatgcttttttttttggtgggggtgcatgggacatactacactaatcagcatcatggtgctaacatttgtgcgtgttacgcaatgtagGGATTGAGAGATGCGTGGGAGGAGGTGAAGCAGATGCGATGCAGAGAGGAGGAGACCAAGCAGAGGGCATCGTTTCTCCAGGAAGGCTTCGCGGCGGCGT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g02070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g02070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G048192_T02 (Zea mays), 3'ss of exon 1
caatcacagatt-aatgcttttttttttggtgggggtgcatgggacatactacactaatcagcatcatggtgctaacatttgtgcgtgttacgcaatgtagGGATTGAGAGATGCGTGGGAGGAGGTGAAGCAGATGCGATGCAGAGAGGAGGAGACCAAGCAGAGGGCATCGTTTCTCCAGGAAGGCTTCGCGGCGGCGT
| ||| | | | | | | | ||| || || || | | | | | | || | || | | ||||| |||| ||||||||||||||||| |||||||| ||||| || ||| ||||||||||||| |||||| || | || |||||| | ||||||||| ||||||
tgacagtgaattcagaggtggtgctgatagaaagggc-tttgaataatggctgacagaactctgtttttttcttctttttgttttgtttaattcaatgaagGGGCTGAGAGATGCGTGGGAGCAGGTGAAGGAGATGAGAGCCAGGGAGGAGGAGACCAGGCAGAGAGCTGCCTTCCTCCAGCACGGCTTCGCGTCGGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactacactaatcagcatcatggtgctaacatttgtgcgtgttacgcaatgtagGGATTGAGAGATGCGTGGGAGGAGGTGAAGCAGATGCGATGCAGAGAGGAGGAGACCAAGCAGAGGGCATCGTTTCTCCAGGAAGGCTTCGCGGCGGCGT
tgctaac putative branch site (score: 1)
taacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatcacagattaatgcttttttttttggtgggggtgcatgggacatactacactaatcagcatcatggtgctaacatttgtgcgtgttacgcaatgtagGGATTGAGAGATGCGTGGGAGGAGGTGAAGCAGATGCGATGCAGAGAGGAGGAGACCAAGCAGAGGGCATCGTTTCTCCAGGAAGGCTTCGCGGCGGCGT
- - - - - - aatgctt
- - - - - - - - - - - - tttggtg
- - - - - - - - - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - acactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcgtg