Sequence
atgc intronic sequence ATGC exonic sequencegtaaggaacttgcatcctcttcattaagggggttagtgcccctgataattatttcacatgtcttgtacatcattatttttgcttttcctcagGAAAAATGTCAAGCAAAAGAAACCGTTAACCAAGGAGAAGAAACAATACACACCCTTTCCACCTCCTCAGCAACCTAGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g51620.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g51620.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G167809_T02 (Zea mays), 3'ss of exon 6
gtaaggaacttgcatcctcttcattaagggggttagtgcccctgataattatttcacatgtcttgtacatcattatttttgcttttcctcagGAAAAATGTCAAGCAAAAGAAACCGTTAACCAAGGAGAAGAAACAATACACACCCTTTCCACCTCCTCAGCAACCTAGCAAG
|||||| | |||| | || || | ||| || || || ||| | ||| || | | ||| | || |||||| ||||||||||| ||||| || ||| ||||||||||||| ||||||||||||||||| ||||| || |||||||||
gtaaggg-cgcacatcatattt-ctattagagttttagcatcttgta--cattgtgtttatctg----attaacaccttttttattttccagGAAGAATGTCAAGCAGAAGAAGCCTCAAACTAAGGAGAAGAAACCGTACACACCCTTTCCACCGCCTCAACAGCCTAGCAAG
upper sequence: LOC_Os01g51620.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G08420.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggaacttgcatcctcttcattaagggggttagtg----cccctgata----attatttcacatgt-cttgtacatcat-tatttttgcttttcct---cagGAAAAATGTCAAGCAAAAGAAACCGTTAACCAAGGAGAAGAAACAATACACACCCTTTCCACCTCCTCAGCAACCTAGCAAG
||| || ||| | |||| || || | |||| | | ||| | || ||| | | | || | || ||||| ||| | |||||||||||| |||||||||||||| || |||||||||||| | ||||||||| || ||||||||||| | ||||||||||
gtatggc-cttctctattcttgatgaataaattgagtgatatcttttaatatatcagtaactcatgagcgcatatatcttatctatttccaatttgatttgacagGAAAAATGTTAAGCAAAAGAAACCCAAAAGCAAGGAGAAGAAGCCATACACACCTTTCCCACCTCCTCAACCACCTAGCAAG
upper sequence: LOC_Os01g51620.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv03s0091g00320.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------gtaaggaacttgcatcct-cttcattaagggggttagtgcccctgataattatttcacatgtcttgtacatcattatttttgcttttcctcagGAAAAATGTCAAGCAAAAGAAACCGTTAACCAAGGAGAAGAAACAATACACACCCTTTCCACCTCCTCAGCAACCTAGCAAG
|| | | | | | ||||| || | ||| | | | | |||| | | || ||||||||| | | | |||| |||||||||||| || ||||||||| | |||||||||||| | ||| |||||||| || |||||||||| ||||||||||
gtatgacatttaccacacccttcttctatacgcatatagtttttaacttcagtatctgtgttgtt--tcaggttttccatttattaacttttttacatcatttgtatatcatttc--cagGAAAAATGTTAAACAAAAGAAAGTTAAGAGCAAGGAGAAGAAGCCATATACACCCTTCCCTCCTCCTCAGCCACCTAGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcccctgataattatttcacatgtcttgtacatcattatttttgcttttcctcagGAAAAATGTCAAGCAAAAGAAACCGTTAACCAAGGAGAAGAAACAATACACACCCTTTCCACCTCCTCAGCAACCTAGCAAG
ccctgat putative branch site (score: 4)
tcattatttttgcttt putative PPT
ataattatttcacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggaacttgcatcctcttcattaagggggttagtgcccctgataattatttcacatgtcttgtacatcattatttttgcttttcctcagGAAAAATGTCAAGCAAAAGAAACCGTTAACCAAGGAGAAGAAACAATACACACCCTTTCCACCTCCTCAGCAACCTAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG