Sequence
atgc intronic sequence ATGC exonic sequencegtaagccatggctatctttctgcatgatcatgctggcactaatattgacaccatgtgagcatcatttcctcctgttgactgttatgttcaatgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g47100.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 2
gtaagccatggctatc-tttctgcatgatcatgctggcactaatattgacaccatgtgagcatcatttcctcctgttgactgttatgttcaatgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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gtaagccatcattgcgacttccactccat-gccctgggaagaataatggtgtcac-----cctcatcttctt-tctcacctctcataat-----tgcagCTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G027851_T02 (Zea mays), 3'ss of exon 4
gtaagccatggctatc-tttctgcatgatcatgctggcactaatattgacaccatgtgagcatcatttcctcctgttgactgttatgttcaatgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG-----------------------------------------------------
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gtaagccatcattgcgacttccactccat-gccctgggaagaataatggtgtcac-----cctcatcttctt-tctcacctctcataat-----tgcagCTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGGTTGGTTGGTTGGTTGGTTGCTGGAACAATCTCATGGACATTTCATTTGAAAC
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
gtaagccatggctatctttctgcatgatcat--gctggcactaatattgacaccatgtgag--catcatttcctcctgttgactgttatgt---tcaat---gtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 4
gtaagccatggctatctttctgcatgatcatgctggcactaatat---tgacaccatgtgagc-atcatttcctcctgttgactgttatgttcaa---tgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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---------------------gtattatattattcaaacttatctatttggcaacttgtcaattgtcaatctgttttgt-gactcaatttttcaaattttttcagCAATTGGTGCAATATTTGCTGCTACAGATTCTGTCTGCACATTGCAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 4
gtaagccatggctatctttctgcatgatcatgctggcactaatat---tgacaccatgtgagc-atcatttcctcctgttgactgttatgttcaatgtg---cagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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---------------------gtattatattattcaaactcatctatttggcaacttatcaattgtcaatctgttttgt-gactcaatttttcaatttttttcagCAATTGGTGCAATATTTGCTGCAACAGATTCTGTCTGCACATTGCAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 4
-gtaagccatggctatctttctgca-tgatcatgctggcactaatattgacaccatgtgagcatcatttcctcctgttgactgttatgttcaatgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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attagagcatgaaaattgcgatgttctcgaaacacattttgctatattttctatttgctccccttatcttatattattgttttcacttcattatttgtagCAATTGGAGCAATTTTTTCAGCTACAGATTCTGTTTGCACCTTGCAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 5
-------gtaagccatggctatctttctgcatgatcatgctggcactaatattg-----acaccatgtgagcatcatttc--ctcctgttgact-gttatgttcaatg---tgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaagttctttgtgttttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
upper sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------gtaagccatggctatctttctgcatgatcatgctggcactaatattgacacca--tgtgagcatcatttc---ctcctgttgactgttatgttcaatgtg-cagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
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gttcgatcttaacacctagataccggttgtgcacaattgttatgtaatgactgtaatgtatggcttacattgtctatcatttgtgccttctgattcctagtgtatttttttctgtacgttagtaaatcgactgagttttggactacttttgtactcccttttgggctttctctgagtctgtttattggcatgacagCTATTGGAGTCATCTTTTCTGCTACCGATTCCGTCTGCACGTTGCAGMapped 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|88358188|gb|CI605113.1|CI605113EST: ATTCAGCAGAATGAACATTGGAACGCTGGATGTAAGGAAAATTTTTCTTG CAATTGGAGCCATCTTTT
genomic: ATTCAGCAGAATGAACATTGGAACGCTGGATGTA-GGAGA-TTTT-CTTGgtaagccatg ... caatgtgcagCAATTGGAGCCATCTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgacaccatgtgagcatcatttcctcctgttgactgttatgttcaatgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
tgttgac putative branch site (score: 3)
atcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccatggctatctttctgcatgatcatgctggcactaatattgacaccatgtgagcatcatttcctcctgttgactgttatgttcaatgtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG