Sequence
atgc intronic sequence ATGC exonic sequence...tttttgaaacaatgggtgttcacactatctgttttcatcaattcaccatgtattttcttgtctttgcatgcacattgatgaattaatctgtgtgcatcagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g48330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g48330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G135085_T01 (Zea mays), 3'ss of exon 2
--tttttgaaacaatgggtgttcacactatctgttttcatcaattcaccatgtattttcttgtctttgcatgcacattga-tgaattaatctgtgtgcatcagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
|| | || | | |||||| | | |||||| || | | | | | | |||||| |||| | || | | | | ||||||||||||| |||||||||||| | |||| ||||||||||||||||| || ||||||||||||||||||||||| | | ||||| | ||||||||
cagttattaagcg-ttattgttcaaaaaagaaacaatcatcag--cattcctccctccccagccatggtatgcacgttgactttctttttatatatatgccagGTAACTATTGTTCAGACAAGAAGGCTGCAGCCGTAAACTGGATAGAAGGTCGTGGGAAATCTGTTGTTTGTGAGGCCAGAGTCAAAGGGGGAGTTGTGCA
upper sequence: LOC_Os02g48330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G136465_T01 (Zea mays), 3'ss of exon 3
-tttttgaaacaatgggtgttcacactatctgttttcatcaattcaccatgtattttcttgtctttgcatgcacattgatgaattaatctgtgtgcatcagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
||||| | ||| || || | ||| || | | | | | |||| ||| | | | | | | | ||||||||||||| |||||||||||| | |||||||||||||||||||||| || ||||||||||||||||||||||| | | ||||| | ||||||||
ccatttgacatggaacaaattcgttgtaataattatgatctgttattagcattcctccctccccagtcatg-gtattcacgttgacctttttttataccagGTAACTATTGTTCAGACAAGAAGGCTGCAGCTGTAAACTGGATAGAAGGTCGCGGGAAATCTGTTGTTTGTGAGGCCACAGTCAAAGGGGGAGTTGTGCA
upper sequence: LOC_Os02g48330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S61_10V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------tttttgaaacaatgggtgttcacactatctgttttcatcaattcaccatgtattttcttgtctttgcatgcacattgatgaattaatc---tgtgtgcat---cagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGT-GCA
| | || | | || || || | | | | || || | | ||| | ||| |||| || | ||| | | | ||| ||||||| | ||| ||||||||||||||||||||||||| ||| | || ||||| || ||||| || |||||||| || || | |||||||| ||| | ||
gtatgtaacacatcctgcttgtgtatgtcatgtctcaaaattagaggtttctatgtatattgatatgctccatccaatggtacaaggtcgtacatgatgctgtt-ctgagacttggtg-gttgtagtatctcttaatga--attggtgtactaacacaatattttcatttgcagGTAATTTTTGTGCAGACAAGAAGCCGACAGCTGTAAATTGGGTTGATGGCCGCGGAAAATCAGTCGTTTGTGAAGCAATCCTGAAAGGAGAAGTTATTGC-
upper sequence: LOC_Os02g48330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S1_155V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------tttttgaaacaatgggtgttcacactatctgttttcatcaattcac-catgtattttc--ttgtctttgcatgcacattgatgaat-taatctgtgtgcat-cagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
|| | || | | ||| || | || | | || | | | | || | | || | || | | || || ||||| ||||| ||||||||| || | ||||| ||||| |||||||| |||||||| || ||||| || |||||||||||||||||||| ||| | || ||||||||||| |
gttcgtgacataccttgattctttgttcctgatgattaatccagaacacgggattgtagttgcataattttctacag-gcatgatagtattagtgcatgcgtagaatctcactagcaagtgggtttacgtgtactaacgtactctgtttgcatgcagGTAACTTCTGTGCGGACAAAAAGCCAACAGCTGTTAACTGGATTGACGGCCGTGGAAAATCTGTTGTTTGTGAGGCAATTCTGAAGGGAGATGTTGTACG
upper sequence: LOC_Os02g48330.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S139_2V6.1 (Physcomitrella patens), 3'ss of exon 2
-tttttgaaacaat--gggtgttcacactatctgtt--ttcatcaattcaccatgtattttcttgtctttgcatgcacattgatgaattaatctgtgtgcat-cagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
||| | | | | |||| || | | ||||| ||| | ||||| | | || | | | || ||||| | ||||||||| || | |||||||| || ||||||||||||||||| || || || || || ||||| ||||||||||| ||| | ||||| || || || |
gtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgcagGTAACTTCTGTGCGGACAAGAAACCAACAGCTGTAAACTGGATTGATGGTCGTGGAAAGTCTGTCGTTTGTGAGGCAATTTTGAAAGGGGACGTCGTACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatgtattttcttgtctttgcatgcacattgatgaattaatctgtgtgcatcagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
aattaat putative branch site (score: 3)
attgatgaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttgaaacaatgggtgttcacactatctgttttcatcaattcaccatgtattttcttgtctttgcatgcacattgatgaattaatctgtgtgcatcagGTAACTATTGCTCAGACAAGAAGCCGACAGCTGTAAACTGGATAGAAGGCCGGGGGAAATCTGTTGTTTGTGAGGCTATTATTAAAGGAGATGTTGTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - -gaaacaa
- - - - - - - - - ttcacac
- - - - - - - - - - - - - -tctgttt
- - - - - - - - - - - - - - - - - - - - -ttcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgaa