Sequence
atgc intronic sequence ATGC exonic sequencegtaagaacactcttgctatttgattgcagttctctttcaacatgatctttctctgtgcacatcttgactgatactctagttattattatttgtatctatccacttgttaacaagatgcataaaatattatgttgctttttcttagGTGCAAGGAAGAGATAGAAATCATGTCAAATTTGTAGCGGAGAAGTTAGGTCTGGATGGCTCTTATATTCCACGCACATATATTGAACAAATTCAGCTGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47860.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G143804_T01 (Zea mays), 3'ss of exon 4
gtaagaacactcttgctatttgattgcagttctctttcaacatgatctttctctgtgcacatcttgactgatactctagttattattatttgtatctatccacttgttaacaagatgcataaaatattatgttgctttttcttagGTGCAAGGAAGAGATAGAAATCATGTCAAATTTGTAGCGGAGAAGTTAGGTCTGGATGGCTCTTATATTCCACGCACATATATTGAACAAATTCAGCTGG
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---------------------------------------------------------------------------gtgagcataatgtttgttgtttacttctttaatgtctgattgtaaaatatgtgcaaatg--tttctttagGTGCAAGGAAGAGATCAACTTTATGTTAAATTTGTAGTGGATCAGTTAGGTTTGGATGGTTCTTATATACTATGCACATATATTGAACAAATTCAGTTGG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 7
gtaagaacactctt-gctatttgattgcagttctctttcaacatgatctttctctgtgcacatcttgactgatactctagttattattatttgtatctatccacttgttaac-aagatgcataaaa--tattatgttgctttttc--ttagGTGCAAGGAAGAGATAGAAATCATGTCAAATTTGTAGCGGAGAAGTTAGGTCTGGATGGCTCTTATATTCCACGCACATATATTGAACAAATTCAGCTGG
|| || | | |||| | | |||| ||| ||| ||| |||| || ||| ||| | |||||| | || | | | |||||| | | | || | ||| | |||||| ||| ||| | ||||| || ||||||||||||||||||| | | |||| |||| ||||||||| |||||||| ||||||| ||||| || |||||||||||||||||||||||||||||||
gtgagcataatctttgttgtttggttgatgtt-tctctcaatgccatttttgtctcaggt--tcttgagttctatttatttcagtattatctttttttaatctcttactgtttaagatgtgcaaatgttatgaccatgcttctttatttagGTGCAAGGAAGAGATCGGCTTTATGTTAAATCTGTAGCGGATCAGTTAGGTTTGGATGGTTCTTACATACCACGCACATATATTGAACAAATTCAGCTGG
upper sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G147430_T01 (Zea mays), 3'ss of exon 7
------------------------gtaagaacactctt-gctatttgattgcagttctctttcaacatgatctttctctgtgcacatcttgactgatactctagttattattatttgtatctatccacttgttaac-aagatgcataaaa--tattatgttgctttttc--ttagGTGCAAGGAAGAGATAGAAATCATGTCAAATTTGTAGCGGAGAAGTTAGGTCTGGATGGCTCTTATATTCCACGCACATATATTGAACAAATTCAGCTGG-----------------------
|| || | | |||| | | |||| ||| ||| ||| |||| || ||| ||| | |||||| | || | | | |||||| | | | || | ||| | |||||| ||| ||| | ||||| || ||||||||||||||||||| | | |||| |||| ||||||||| |||||||| ||||||| ||||| || |||||||||||||||||||||||||||||||
caacttaacagacaatatatacaagtgagcataatctttgttgtttggttgatgtt-tctctcaatgccatttttgtctcaggt--tcttgagttctatttatttcagtattatctttttttaatctcttactgtttaagatgtgcaaatgttatgaccatgcttctttatttaggtgcaaggaagagatcggctttatgtTAAATCTGTAGCGGATCAGTTAGGTTTGGATGGTTCTTACATACCACGCACATATATTGAACAAATTCAGCTGGAGAAATTGATTAATGATGTTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatctatccacttgttaacaagatgcataaaatattatgttgctttttcttagGTGCAAGGAAGAGATAGAAATCATGTCAAATTTGTAGCGGAGAAGTTAGGTCTGGATGGCTCTTATATTCCACGCACATATATTGAACAAATTCAGCTGG
tgttaac putative branch site (score: 2)
tgttgctttttctt putative PPT
ataaaatattatgttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaacactcttgctatttgattgcagttctctttcaacatgatctttctctgtgcacatcttgactgatactctagttattattatttgtatctatccacttgttaacaagatgcataaaatattatgttgctttttcttagGTGCAAGGAAGAGATAGAAATCATGTCAAATTTGTAGCGGAGAAGTTAGGTCTGGATGGCTCTTATATTCCACGCACATATATTGAACAAATTCAGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG