Sequence
atgc intronic sequence ATGC exonic sequence...taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g02510.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G34760.4 (Glycine max), 3'ss of exon 1
taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgt---aggtaagGTAAG-CCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| | | | | | || | || | || | || | || ||| || || | |||| | ||| ||| ||| ||||||| || ||||||| ||||| ||||| || ||||| || || |||||| |||||||||||||||||||| ||||| |||||||| ||||| || || ||
ttgttagttatctgctatt-ttacactatcttgtgctta-tcctattaccttattacataat-ctaacctgttgtcgtggttgactttaatgtgtaaggtaagCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCACGGAA-
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G14640.1 (Glycine max), 3'ss of exon 1
-----taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgta-ggtaagGTAA-GCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| ||||| | ||| | | ||| | ||| | |||| | ||| | || ||| || || ||||| |||||| || |||||||| ||||| ||||| || ||||| ||||| |||||| |||||||||||||||||||| ||||| |||||||| ||||| || || ||
gtgattgatctgctatggttacgctttcttgtgcttatccaattaccttattacataatctaa-----cttgttgtc-gtggatgacctgttatgtgtaaggtaagCCAAAGCCATGGTTAAGCATAACAATGTTATCCCCAATGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACCTGGTTCAATCAGCCAGCACGGAA-
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G08090.1 (Glycine max), 3'ss of exon 1
-----taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgat-ttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
|| | | | || ||| | ||| | | | || | | | | | || || || ||| |||| ||| | ||| | ||| |||||| ||||| ||||| |||||||| ||||| ||||||||||||| ||| |||||||| |||||||| ||||| ||||| || || || || || |||
catagtattttaattggggtttgcagctgatttgtcttttatacatgatcatatgttgac-cctgttgttt----tttttgttcttttattgttgtcatttgta-gGTAAGATATGGTTAAGCATAACAACGTTATCCCCAATGGGCACTTCAGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCACGGAAG
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
--taatctggtgtggatttttgctgca-actgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgt---aggtaagGTAAG-CCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| || || | | | | ||| | | || | || ||| || || | |||| | ||| ||| ||| ||||||| || ||||||| ||||| ||||| || ||||| || || |||||| |||||||||||||||||||| ||||| |||||||| ||||| ||
gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataat-ctaacctgttgtcgtggttgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA------
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G17370.1 (Glycine max), 3'ss of exon 1
taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcat-gatgcttatggtttgtgtttgtttgatttggtgtaggta--agGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| | || || || | ||| | | | || | | | | || || || ||| | | | || ||| |||| | |||||||| ||||| ||||| || || || ||||| |||||||||||| ||| |||||||| |||||||| ||||| ||||| || || || ||||| |||
---tatagtatgttaattggggtttgtagttgatttgtcttttttatatgatcttatgtcgaccctgttgttttatttgttcttttattgctgtaatttgtagGTAAGCAATGGTTAAGCATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAG
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G14640.2 (Glycine max), 3'ss of exon 1
----------taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgta-ggtaagGTAA-GCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| ||||| | ||| | | ||| | ||| | |||| | ||| | || ||| || || ||||| |||||| || |||||||| ||||| ||||| || ||||| ||||| |||||| |||||||||||||||||||| ||||| |||||||| ||||| ||
tgtttgtgattgatctgctatggttacgctttcttgtgcttatccaattaccttattacataatctaa-----cttgttgtc-gtggatgacctgttatgtgtaagGTAAGCCAAAGCCATGGTTAAGCATAACAATGTTATCCCCAATGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACCTGGTTCAATCAGCCAGCA------
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G49010.1 (Arabidopsis thaliana), 3'ss of exon 1
------taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaagga-atcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGG---TGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| | || || |||| || |||||||| | ||| |||| ||| || |||| || ||||| | | | || | | || | ||||||||||||| || ||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||||||||| ||| |
ttttgtttttgaagtttgaggttttatcatt-tgatttccttgagctgtttaaagtttcatcatttgat--ttaaagt--gtgtctgattgatgtttttt-ggcagCTTGAGTTGAAGAAATGAAGCACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAG----
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
taatctggtgtggatttt-tgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG------
| ||| | || | | | | | | | || | | | | | | | || | | | || |||| || || | |||||||||||||||| ||||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| ||| | |||
-----taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagA--AAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
--taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| | | | |||||||| || || || ||| | | || | | | || || | |||||||| || | | ||||||||||||| ||||| ||||| || | || ||||||||||||||||| || |||||||| |||||||| || ||||| ||||| || || |||||
tcttttttcattcagatttttg-tgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttaca-gGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S21_106V6.1 (Physcomitrella patens), 3'ss of exon 1
------taatctggtg--tggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
|| || | | || | ||| || ||||| | | | | || ||||| || | || | | | |||| | | ||||||||||||| ||||||||||| || ||||| |||||||||||| |||||||||||||||| | ||| ||||||||||||||||| |||
gccctccgccttgatgcttcagtagtttgcatggtgcattgtatcagggtttaggtctgtgggaaaaaaaacgtagggtttctgatggtgttgct---cgcagGTCTAGCA--CCATGGTGAAGCATAACAACGTCATTCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACTTGGTTCAACCAGCCCGCACGC---
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S47_277V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------------------taatctggtgtggatttttgctgc--aactgttagtaag--agctgttaggaaggaatcgcatgat-gcttatggtttgtgtttgtttgatttggtgtaggtaagGT--AAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| |||| || || | | ||| | | | || | | || || ||||| | | | ||| | | | |||| | | | || || ||||||||||||| ||||| |||||||| || || || ||||||||| ||||||| |||||||| | ||| ||||||||||||||||| |||
gtgtgcctcgccgctcatcttaacattgtacagcttcataggcttccagttgggaaggagtttgtggttgcttgtgcaattccttgtgggagatggtctgtccaaagttcttccccctaaacgggaggcgatctagttctcctgaggggtgtgcatggttgttgatgtatactaagtttttggtcatcaccactcagGGACGAAACCATGGTGAAGCATAACAATGTCATCCCTAACGGACATTTCAAGAAGGACTGGCAAAACTATGTGAGGACGTGGTTCAACCAGCCCGCTCGC---
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S459_9V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaa---ggaatcgcatgatgcttatggtttgt--gtttgtttgatttggtgtaggtaagGTAAG--CCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| | | || || |||| | || | |||||| | | | | | | | || | || ||| || | ||| | || |||||||||||| ||||| |||||||| || || |||||||||||| |||||||||||||||| | ||| ||||||||||||||||| |||
gtatgctggcttgctttcctttgcattgcacagctgcgtaaggttgtggctggggatcgtgctgtaagactcatttctttcaggagaattcagctggagctcagcttcggagctgaaggcgacttaggtttgtttagtttttcatgcccactaaactgcttgtcgtgaaaaacgtagGACCAGAATCATGGTGAAGCATAACAATGTCATCCCCAACGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCACGC---
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S459_9V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaa---ggaatcgcatgatgcttatggtttgt--gtttgtttgatttggtgtaggtaagGTAAG--CCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG---
| | | || || |||| | || | |||||| | | | | | | | || | || ||| || | ||| | || |||||||||||| ||||| |||||||| || || |||||||||||| |||||||||||||||| | ||| ||||||||||||||||| ||||||
gtatgctggcttgctttcctttgcattgcacagctgcgtaaggttgtggctggggatcgtgctgtaagactcatttctttcaggagaattcagctggagctcagcttcggagctgaaggcgacttaggtttgtttagtttttcatgcccactaaactgcttgtcgtgaaaaacgtaggaccagAATCATGGTGAAGCATAACAATGTCATCCCCAACGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCACGCAAGAAG
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S58_38V6.1 (Physcomitrella patens), 3'ss of exon 1
-taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggt--aagGTAAGC--CATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| ||| |||| | | || | || | | | | | | | | | ||||| | ||| || | ||| || | | ||| || |||||||||||| || || || ||||| ||||| |||||||||||| |||||||||||||||| | ||| |||||||||||||||||||||
ttgtgatggagtggcgtgccgatgttgttcttgtctcgcattcctcatatagggtttaagggt--ttatgacataacgatgtcggagtcggtctattttcagGGTTGGCACCATGGTGAAGCATAATAATGTTATCCCCAATGGTCACTTCAAGAAGGACTGGCAGAACTATGTGAGGACCTGGTTCAACCAGCCCGCCCGC---
upper sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S126_52V6.1 (Physcomitrella patens), 3'ss of exon 1
taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagG---TAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
| ||| |||| | || || |||| | | || | | | ||| | || | | | | ||| | ||||| || | | | | |||||||||||| ||||| || ||||| ||||| |||||||||||| ||||||| |||||||| | ||| ||||| ||||||||||||||||
tgtgatggagtggcgtatttttgtg-ttgttgttgtaattcgtgaagcaataattagggtcggattgttgatgtcgcaatttttgtgatgtgtatgtgaagAGTTGAAACATGGTGAAGCATAACAATGTTATCCCCAATGGCCACTTCAAGAAGGACTGGCAAAACTATGTGAGGACCTGGTTTAACCAGCCCGCCCGCA--Mapped 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|58595081|gb|CF993389.1|CF993389EST: CGCCGCCGCCTCGCCGCCCAAGGTAAG
genomic: CGCCGCCGCCTCGCCGCCC-----AAGgtagggtgcc ... tgtagg
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
gtttgat putative branch site (score: 5)
tttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG
- - ctggtgt
- - - - - - - - - tgctgca
- - - - - - - - - - - - - - - - - - -agctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct