Sequence
atgc intronic sequence ATGC exonic sequence...tcttgaggtgcggaaacttaatctccattgttgtttgaatttggtttgggacggtctaagtttttctgctaaatctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52479.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033724_T02 (Zea mays), 3'ss of exon 2
--------------------------tcttga-ggtgcggaaacttaatctccattgttgtttgaatttggtttgggacggtctaagtttttctgctaa---------atctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
| | || | | || | ||| |||| | | | |||| | || | || | ||| ||| | || | ||||||||| |||||||| |||||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||| || |||||||| || |||| |||||| |||| ||||| || |
gtagggaagctgtaattcatacgtattttagatgattgggttagttatgctcccaaacaatgctactgaagttttgtactttggaattctttttgccatggtctggatatttatcacttagtcggatcattgacagGGTCCAGGAGGTATTTGGTGTGATGTTGATGTTGTTGAGTTTTCGTACTACGGTGCTCCAGCTCAAACTCCAAAAGTGCAAATATTCACAGAGCTCGTGG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033724_T01 (Zea mays), 3'ss of exon 1
tcttgaggtgcggaaacttaatctccattgttgtttgaatttggt---ttgggacggtctaagtttttctgctaa-atctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
|| | | | || || || | | | ||| || |||| | | | | | | | || | ||||||||| |||||||| |||||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||| || |||||||| || |||| |||||| |||| ||||| || |
---tgggttagttatgctcc-caaacaatgctactgaagttttgtactttggaattctttttgccatggtctggatatttatcacttagtcggatcattgacagGGTCCAGGAGGTATTTGGTGTGATGTTGATGTTGTTGAGTTTTCGTACTACGGTGCTCCAGCTCAAACTCCAAAAGTGCAAATATTCACAGAGCTCGTGG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G102346_T01 (Zea mays), 3'ss of exon 2
-----------------------------------tcttgaggtgcggaaacttaatctccattgttgtttgaatttggt---ttgggacggtctaagtttttctgctaa-atctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
|| | | | || | || || || | | ||| || ||| | | | || | | || | || ||||||||| |||||||| |||||||||||||||| |||||||||||||||| |||||||| || ||||||||||||||||| ||||||| || |||| ||||||||||| |||||||||||
gtaggggaactgtaattagtatgtattttggatgatcgggttagccatgctcccaaacaacaatgctggtgaagttttgtactttgaaaatcttttcgtcgtggtctgaatagctatcacttagtcggatcattgacagGGTCCAGGAGGTATTTGGTGTGATGTTGACGTTGTTGAGTTCTCGTACTACGGTGCACCAGCTCAAAATCCAAAAGTGCAAATGTTCACTGAGCTTGTTG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G34800.1 (Glycine max), 3'ss of exon 2
tcttgaggtgcgga---aacttaatctccattgttgtttgaatttggtttgggacggt--ctaagtttttctgctaaatctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
|||| | | | |||| || | ||| || || ||||| | | |||| | |||| || | || |||| || | ||||||| || |||||||||||||||||||| |||||||| || || || || || |||||||| || ||||| |||||||| ||| | | | ||||||| ||
tcttaaagcaacaatggaactaaagcaatattatttaagatcttatgtttgttataatttctaattgaagatgctgaagttatctcttatttcca-----aacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
tcttgaggtgcggaaacttaatctccattgttgtttgaatttggtttgggacggt--ctaagtttttctgctaaatctt--tcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
| | |||| | | ||| || || ||||| | | |||| | |||| | ||| | || | ||||||| || |||||||||||||||||||| |||||||| || || || || || |||||||| || ||||| |||||||| ||| | | | ||||||| ||
---agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctc-ttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G45030.2 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------------------tcttg-aggtgcggaaacttaatctccattgttgtttgaatttggtttgggacg---gtctaagtttttctgctaaatc----tttcacttagttggatcat----taacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
| || |||| | | | | | ||| | | || || | | || | || ||| | |||| ||| |||| | | ||| | | | ||||||| ||||| |||||||||||||| ||||||||||| ||| || || |||||||| || ||||||||||||||||| ||| | ||||||||||
gtgagatatctcttgcctatgatactttacttataatcgtttgcttgtgcttgaaagagtatattggaacttttagtaatgtaggtactacagcatggaacctattataga--aaactttactaatgccgcctatttatgttgccttctggaatcctttttttacttcatagtatcttgctttgatagGGTCCTGGAGGAGTTTGGTGTGATGTAGATGTTGTTGAGTTTCAATATTATGGTGCACCTGCGCAAACACCTAAAGAGCAGGTGTATACAGAGCTTGTTG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0011g01870.t01 (Vitis vinifera), 3'ss of exon 3
tcttgaggtgcggaa-acttaatctccattgttgtttgaatttggtttggg-acggtctaagtttttctgctaaatctttcacttagttggatc-attaa-cagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
| || || | || || || ||| || | |||| | || ||||||| || || | | || ||| ||| | ||||| |||||||| || ||||||||||| |||||||| ||||| || ||||| |||||||| || | |||||| ||||| ||| ||| | ||| ||||| |
tactgcaacttggtatggttcatatc--ttgacagggaaactaaacttggatattgttcaagttttcttg--gaagttgaaatgcctttaaatctattgagcagGGACCAGGAGGCGTATGGTGTGATGTGGATGTTGTGGAATTCTCTTACTATGGTGCACCTGCACCAACACCCAAAGAACAATTGTATACTGAACTTGTCG
upper sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ25881 (Selaginella moellendorffii), 3'ss of exon 1
tcttgaggtgcggaaacttaatctccattgttgtttgaatttggtttgggacggtctaagtttttctgctaaatctttcacttagttggatcattaa-cagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
|| | | || | || ||| | || | || | | | | | | || || ||||| || || || |||||||||||||| ||||| |||||||| |||||||| || || || | ||||| || |||||||| | | ||||| || |
-----------------------------gtaactagtgcatg--taaaaccgctctcggcttcttaactcgctggtgaagt-aacagtttctctactcagGGGCCTGGGGGAGTTTGGTGTGATGTAGATGTGGTTGAATTCTCGTACTATGGCGCTTCGACCGTGACACCAAAGGAGCAAATTTACTCCGAGCTGGTCGMapped 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|58670093|gb|CK058779.1|CK058779EST: TTCATAAGAAGTGGCTTAATCCAGCACAATGTCTTCCTGCTATTCTTGAG GGTCCAGGAGG
genomic: TTCATAAGAAGTGGCTTAATCCAGCACAATGTCTTCCTGCTATTCTTGAGgtgcggaaac ... tcattaacagGGTCCAGGAGG
EST:
gi|58659200|gb|CK047880.1|CK047880EST: TTCATAAGAAGTGGCTTAATCCAGCACAATGTCTTCCTGCTATTCTTGAG GGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTAC
genomic: TTCATAAGAAGTGGCTTAATCCAGCACAATGTCTTCCTGCTATTCTTGAGgtgcggaaac ... tcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTAC
EST:
gi|58605986|gb|CK034019.1|CK034019EST: TTCATAAGAAGTGGCTTAATCCAGCACAATGTCTTCCTGCTATTCTTGAG GGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTAC
genomic: TTCATAAGAAGTGGCTTAATCCAGCACAATGTCTTCCTGCTATTCTTGAGgtgcggaaac ... tcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgggacggtctaagtttttctgctaaatctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
tgctaaa putative branch site (score: 2)
taagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgaggtgcggaaacttaatctccattgttgtttgaatttggtttgggacggtctaagtttttctgctaaatctttcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT