Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatttgtttatgcagttatttgctagttcaaactgtgcaaattactaaattgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g02050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 2
gtaatcatttgt----ttatgc--agttatttgctagttcaaactgtgcaaattactaaa-ttgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
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gtatacatttgtcgtcttaatcttagctgtttaccggat-gtattatgcaaattgctgaagtttatcatgca-cagGTTTTAGAAGATGGAGTGCTTGATCCTGAGACTACTATAGTGTCTATATTTCCCTCACCAATGCATTATGCTGGTCCAACAGAAGTGCAGTGGCATGCAA
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G05020.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------------------------------------gtaatcatttgtttatgcagttatttgctagttcaaactgtgcaaat-tactaaattgatcatatggc---agGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
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gtaattcccattgttcttctcaaaaaacaaagactaatcataatgtgcatgtgctacaacaatagatgttaaaaaaatgaccttgaaaagtgattgaactatcactcaaatttagcaatctactcattttgtaattgcacaatccatggaattttattctaccaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATCGTTGCCATATTTCCATCACCTATGCATTATGTTGGTCCAACTGAAGTACAGTGGCATGCCA
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------gtaatcatttgtttatgcagttatttgctagttcaaactgtgcaaattactaaa----ttgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
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gtaattcccattgttcttctcaaaaaacatagggtaatcataatgtgcatgtgctacaacaatatatgttcaaaaatgacctcaaaaagtgattgaactgtcattcaatttcagtaatctactcattttgtaattgcacaatccatggaattttatcctataaagttctttgcttcttcttagGTCCTAGAAGATGGAGTTCTTGATCCTGAGACTACCATAGTTGCCATATTTCCATCACCTATGCATTATGCTGGTCCAACTGAAGTACAGTGGCATGCAA
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------gtaatcatttgtttatgcagttatttgcta-gttcaaactgtgcaaattactaaattgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
| || ||| | | ||||| | | | | | || | | || || || ||||| |||||||||| || ||||| || |||||||||| || || || || || || |||||||| |||||||||||||| ||||| |||||||| || |
gtgcatatttgctgttgtttccgagttcgttttcctcataaagaatttgttgtaaagagagattatgatttgatttgcttatgatgtg-tagGTTCTAGAAGATGGAGTTCTTGACCCGAAGACTACTATTGTCTCGATCTTTCCGTCACCGATGCACTATGCTGGTCCAACTGAAGTTCAATGGCACGCCA
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------gtaatcatttgtttatgcagttatttgctagttcaaactgtgcaaattactaaattgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
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ttttattttagtcttttgacaagtttatgaaacttaaaaatttaattgtcatgtgttgtccaaagttcaattttcttattca--aattttatttttggacagGTCCTAGAAGATGGAGTCCTTGATCCTGAAACTACCATTGTGGCTATATTCCCATCACCTATGCATTATGCAGGCCCAACTGAAGTACAATGGCATGCCAMapped 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|33796395|gb|CF324064.1|CF324064EST: CGAAAGCTGATGATGTCCCGTTGCCTGTGAGAATGGAACAACACAGCAAG GTCTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTC
genomic: CGAAAGCTGATGATGTCCCGTTGCCTGTGAGAATGGAACAACACAGCAAGgtaatcattt ... catatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcagttatttgctagttcaaactgtgcaaattactaaattgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
aaattactaaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatttgtttatgcagttatttgctagttcaaactgtgcaaattactaaattgatcatatggcagGTTTTAGAAGATGGTGTCCTTGATCCTGAGACTACTATAGTGTCTATTTTCCCCTCCCCGATGCATTATGCTGGTCCAACAGAAGTGCAATGGCATGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT