Sequence
atgc intronic sequence ATGC exonic sequencegttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttcaaccattaatcattactgagtttctgatatatggtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g04230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g04230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G374088_T01 (Zea mays), 3'ss of exon 2
gttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttca-accattaatcattactgagtttctgatatatg--gtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
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----------------------------------------------gtttgttaggaacatat-taaataattcacctcatcatcaacatcaacagtcacccctatctttctgatatatgtaacctataacactgcagCCCATGTATTTCATCGTGATTTAAAGCCCAGGAACATACTGGCCAATTCAGACAGCAAACTAAAGATCTGCGACTTTGGACTTGCACGTGCATCATTTAA
upper sequence: LOC_Os02g04230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP02733 (Chlamydomonas reinhardtii), 3'ss of exon 4
gttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttcaaccattaatcattactgagtttctgatatatggtttaacttgtct--cagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
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------------------------------------------tgcagggtggtggggcggtgctggcggtgcaccggcgctgaccctgtccctcctcctccccgctcgtcccgctccgggtccctccccccctgcagccaagGTGTTCCACCGCGACCTCAAGCCCAAGAACATCCTGGCCAACTCCGACTGCAAACTCAAGATATGTG----------------------------
upper sequence: LOC_Os02g04230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
gttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttcaaccattaatcattactgagtttctgatatatggtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
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-------------tgaaaatgtaacta--tatttcaagaaga--------atagtggat---tatgatctaatgaatgtgtgtctcg---tttggatgttgacgtgcttc---tatttgggtga---tgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
upper sequence: LOC_Os02g04230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttcaaccattaatcattactg-agtttctgatat----atggtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
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---------------------------------tcac-aactctcactgtacaaaagactgatgggatgtg-----gtcctttttggatttctgtctgtttttgtggatgttgacgtcttcatgtttgggattgt-tcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAGMapped 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|117220894|gb|CT845593.1|CT845593EST: CCGTTTTTTCTTGTACCAACTTCTTTGTGCTCTCAAGTACATACATTCAG CTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAG
genomic: CCGTTTTTTCTTGTACCAACTTCTTTGTGCTCTCAAGTACATACATTCAGgttagtgatg ... cttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAG
EST:
gi|58655691|gb|CK044371.1|CK044371EST: CGTTTTTTCTTGTACCAAGTGCGTTTGTGCTCTCAAGTACATACATTCAG CTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAG
genomic: CGTTTTTTCTTGTACCAACTTC-TTTGTGCTCTCAAGTACATACATTCAGgttagtgatg ... cttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttcaaccattaatcattactgagtttctgatatatggtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
gtttaac putative branch site (score: 3)
cttgtctc CT-rich tract
attaatcatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttcaaccattaatcattactgagtttctgatatatggtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA