Sequence
atgc intronic sequence ATGC exonic sequencegtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g29830.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G137541_T01 (Zea mays), 3'ss of exon 2
gtacatattt-------cagtgttctagtatggacagtat-gctttgcaattggcatcagta-cgttgaaa---ctgagtatt---ttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
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gtacggatttggtcacccaacgttttgccgcttgctggatcgctctgaaactgacatgaccggtcctgaaaaccctggctgttgcattgcatcttccctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTTCTGCAGGACCTTGTTCCTGGTTGCAGCAAA
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
------------------------gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaa----actgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG----------------------------------
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gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgc--ggtctggaattcacaccccaatgtttaaccctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G818643_T01 (Zea mays), 3'ss of exon 2
------------------------gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaa----actgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
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gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgc--ggtctggaattcacaccccaatgtttaaccctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAA
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG----------------------------------
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---------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
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---------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 3'ss of exon 3
gtacatatttcagtg-----ttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
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gtaagatttttcatggatagttttagttttgatag-aagcaattctattgtcct-agtc--ttggagttaaagctggtggaccttgatgacagGTAAGAAGGGAAAAGATCAGTGAAAGGATGAAGTTTCTTCAAGACCTGGTACCTGGTTGCAGCAAG
upper sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S145_69V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaac-tgagt-attttacgtttcg-tgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG----------------------------------
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gtaaaatcccagatcccaagtttccttctcgattcgattcgattcataacctcaactattagtatt--ctgaactcgtcacacatctctgtagcactccctgacgtgagtcatcatgttgtacgctcctcagGTTCGCAGGGAGAAGATCAGCGAGCGGATGAAGTATCTTCAGGACCTAGTTCCTGGCTGCAATAAAGTGACCGGCAAGGCAGTGATGCTCGACGAGATCAMapped 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|218493872|gb|FG957202.1|FG957202EST: TCCGGGCTCGGCGTGGCCAGGCAACCAACAGCCACAGCTTAGCAGAAAGG TTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTT
genomic: TCCGGGCTCGGCGTGGCCAGGCAACCAACAGCCACAGCTTAGCAGAAAGGgtacatattt ... tcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
agtatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG