Sequence
atgc intronic sequence ATGC exonic sequence...tactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g44090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g44090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G150841_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------tactagtaatttaactacttctcttaattaattata-gcttggatgatttctagctaattaatcaatcaaacaggaaatt--aatcagcttgaat-------tgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
| | | ||| | || |||| | | || |||||| | | | ||||| | | |||| || ||| | ||| |||||||||||||||||| | ||||||||||| ||||||||||||||||| ||||||||||||||||| ||| ||||||||||||| || |||||||| |||
gtaggtggtgccacagtggcaggccatgcatacagcagatccccggcccggccagtttcttttatttattagctgtgtgcgatgatgatgatgaatgatccatccaatcggggatgtaattctgttcgttttgcacgtacgaatgacacagGTGGTCTCAGATTGCTTCGCAGCTGCCGGGGCGGACGGACAACGAGGTGAAGAACTTCTGGAACTCGTACGTCAAGAAGAAGCTCCGGCAGCGCGGGATC
upper sequence: LOC_Os07g44090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
tactagtaatttaactacttctcttaattaatt-atagcttggatgatttctagctaattaatcaatcaaacag-gaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC-
| || ||| | || | | | | | | | | ||| || | ||||| | || |||||| ||| | ||||||||| |||||||| | || || || || || |||||||||||| ||||||||||||||||||| | ||||||||||||||| ||| ||| || |
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttattt--ttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGC-AGCATGGGAATC
upper sequence: LOC_Os07g44090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 2
--tactagtaatttaactacttctct-taattaattatagcttggatgatttctagctaattaatcaatcaaaca-ggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
| || || | | |||| | ||| | | | || | | || | |||| ||| |||| || |||||||||||||||||| ||||| | || || || || |||||||| |||| |||||||||||||| | |||||||||||||||||| | |||||||
ctgagacacgataaggtcacatgttggtaataagctatcccccccccccccccccccctgctagttgggctaatgcagcaattgatccccttgcatg----cagGTGGTCTCAGATTGCAACTCAGTTACCAGGCCGCACCGACAACGAAATCAAAAACTTCTGGAACTCCTGTATCAAGAAGAAGCTTCGCAACATCGGCATC
upper sequence: LOC_Os07g44090.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S277_14V6.1 (Physcomitrella patens), 3'ss of exon 2
-----tactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
| || || | | | | | |||| ||| || || | | | | ||| ||| || ||| || || | ||||||||| |||||||| | ||||| || || || ||||||||||| | || |||||||||||||||| ||||||||||||||| || | |||||||
tcatcgatgagaggcagaagggccggattgtagtctctgcagct-acatgtgctccttgcaaatgttgagttaaagcagaatttgatc---ctgtat-aatgcagGTGGTCACAGATTGCAACCCAGCTACCAGGCCGCACGGACAACGAAATAAAAAACTTCTGGAACTCTTGCATCAAGAAGAAGCTGCGTAACATCGGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
aattaat putative branch site (score: 3)
taattaatcaatcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tactagtaatttaactacttctcttaattaattatagcttggatgatttctagctaattaatcaatcaaacaggaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - gcttgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcttg