Sequence
atgc intronic sequence ATGC exonic sequence...ggtcattgatggcttaatacaaagattcctagttagctgataattaccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g15580.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G148118_T02 (Zea mays), 3'ss of exon 6
-ggtcattg--atggcttaatacaaagattcctagttagctgataattaccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
||| | || ||| | || | ||| | | || ||| || | || | |||| | | ||||| || | ||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||
gattcaatattatatctttctcttaatgtcatgttttaatgaacagttgccg--tagcttactatgttattagcatggttaaccttttgct-gctgtttgcagGTTCCAATGTTTGAAAACATGGATGAACAGCTGTTGGATGCCATGTGTGATCGTCTAAAGCCTATGCTGTACACAGAAGGAAGCTGCATCATTCGCGAAG
upper sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G066269_T01 (Zea mays), 3'ss of exon 1
-----ggtcattgatg-gcttaatacaaagattcctagttagctgataattaccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
| ||| | ||| | | | || | || || || | | | | | | || | | || | ||| | |||||||||||||||| ||||||||||| || | ||| |||| || ||||| || ||| | || |||||||||||||||||||| ||| |||| |||||||||
tcataaggaattactttgctctttgtaccattcaatacgtgagaga-aagactcgaccctatcatgattccgatatgacttacacgccgtttacaa-----tgcagGTTCCAATGTTCGAAAACATGGACGACCAACTCCTGGACGCAATGTGCGACCGTGTGAAACCCATGCTGTACACAGAAGGAAGCCACATCGTTCGCGAAG
upper sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G41610.2 (Glycine max), 3'ss of exon 7
--ggtcattgatggct-taatacaaagattcctagttagctgataattaccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
|| | || | | || ||| || || || | || || || |||||| ||| | | || |||| || | | | | |||| ||||||||||| |||||||| ||| | || |||||||| |||||||| || || ||||| |||| |||||||||| |||||||| | || ||||
taaaccaattattgttgctattggaagttttgaagctatagttcattttccatgtaatattttagt-aataactaaaatctttctcttgc--atgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTATACACAGAAGAAAGCTGCATTGTCCGGGAAG
upper sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G44430.1 (Glycine max), 3'ss of exon 6
ggtcattgatggcttaatacaaagattcctagttagctgat---aattaccggctatccctttagttaattaatcccttcattctttt-tctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
|| | || | || | || | || | | | || | | || || |||| || || || | || | | | || |||| ||||||||||| || ||||||||| || | |||||||| ||||||||| | || ||||| | || || || || |||| ||| |||| ||||
-gtgagtgtcactcataatcatgtctccccatctattttttttaatctaactgtagtctaattgtgtaatgaacatttttatgttcttattttattgctt-tagGTGCCAATGTTTGAGAAAATGGATGAGCAGTTGTTGGATGCAATGTGTGATAGACTGAAGCCAGTCCTTTATACTGAGAAGAGCTACATTGTTCGTGAAG
upper sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 7
ggtcattgatggcttaat--acaaagattcctagttagctgataatta-----ccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
|||| | || | | |||||| | ||| || || || |||||| | ||| | || |||| ||| || | | |||| ||||||||||| |||||||| ||| | || |||||||| |||||||| || || ||||| ||||||||||||||| |||||||| || ||||
-----ttgaaaagtaaaccaattatcgttcctattggaagaatagttggttttccatgtaatattttagtaa--taaccaaatccttctcttttgcatgaacttaagGTGCCAATGTTTGAGAACATGGACGAGCAACTTTTGGATGCTATGTGTGACCGACTCAAGCCAGTGCTGTACACAGAAGAAAGCTGCATTGCCCGGGAAG
upper sequence: LOC_Os02g15580.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv16s0050g02560.t01 (Vitis vinifera), 3'ss of exon 7
ggtcattgatggcttaatacaaagattcctagttagctgataat-taccggctatccct-ttagttaattaatcccttcattctttttctcaccatt-tgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
| || || | | | | | |||| || |||| ||| || | || || || | ||| |||| | | |||| | |||| |||||||| ||||| ||||||||| | || ||||||| |||||||| ||||| ||||| ||||||||||||| |||| |||| | || || |
-ttggttttcagcattgtgtgttgtcttcaagttgattggtaatgcaccattaattattactaaaccatggat--ttacatctttttcttaaacattgttaagGTGCCAATGTTCGAAAAGATGGATGAGCAACTGATGGATGCAATGTGTGACCGTCTCAAGCCAGCACTGTACACAGAAGATAGCTACATCGTCCGGGAGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|27547551|gb|CA765641.2|CA765641EST: ATCTTAGGAGAGAGATAAAGAGGCATCTTTGCCTGTCGCTTCTCATGAGG GTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGAT
genomic: ATCTTAGGAGAGAGATAAAGAGGCATCTTTGCCTGTCGCTTCTCATGAGGgtattttctc ... ccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
ttctcac putative branch site (score: 2)
tcccttcattcttttt CT-rich tract
tttagttaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtcattgatggcttaatacaaagattcctagttagctgataattaccggctatccctttagttaattaatcccttcattctttttctcaccatttgcagGTTCCAATGTTTGAAAACATGGATGAGAAGCTCTTGGATGCCATGTGTGATCGTCTAAAGCCCATGCTGTACACAGAAGGCAGCTGCATCATTCGCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - -ttgatgg
- - - - - - - - - acaaaga
- - - - - - - - - - - - - - - - - -gctgata