Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGGTAAGACAAGCTAGACCACTTAAAGTCGTGTCCAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g53880.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g53880.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G057067_T02 (Zea mays), 3'ss of exon 4
gtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaac--aacaaaaggacactgccacca-taattt----------atattaggca--------ccaccaaaccatctaaattatttttcctgttctccaattcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGGTAAGACAAGCTAGACCACTTAAAGTCGTGTCCAAA
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--------gtaagcttcctctgtcatttacggtccaaccgcaccctaccaacagaaaaacttctctaaaactgaatcgtcaaatactgctaacactaacttgaagaatgaaatatagTACAGGCCTACTTTGTTGCACCATCTGAA--GCCTTCCTTTGTATGTGATCCCTGCAGTGTGTTTGTGTCAACTGCTAAAAGGCTGAGGGTTTTGAGGAGCT--------------------------------------------------------
upper sequence: LOC_Os01g53880.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G057067_T01 (Zea mays), 3'ss of exon 4
gtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaac--aacaaaaggacactgccacca-taattt----------atattaggca--------ccaccaaaccatctaaattatttttcctgttctccaattcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGGTAAGACAAGCTAGACCACTTAAAGTCGTGTCCAAA
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--------gtaagcttcctctgtcatttacggtccaaccgcaccctaccaacagaaaaacttctctaaaactgaatcgtcaaatactgctaacactaacttgaagaatgaaatatagtacaggcctactttgttgcaccatctgaa--gccttcctttgtatgtgatccctgcagTGTGTTTGTGTCAACTGCTAAAAGGCTGAGGGTTTTGAGGAGCTCGGAGCTTGCCAAAGGTTTGGTAGG---CACAAGGCCACCTCAG------------
upper sequence: LOC_Os01g53880.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G057067_T04 (Zea mays), 3'ss of exon 4
------------gtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaac--aacaaaaggacactgccacca-taattt----------atattaggca--------ccaccaaaccatctaaattatttttcctgttctccaattcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGGTAAGACAAGCTAGACCACTTAAAGTCGTGTCCAAA
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gtaggggacgtgccgtggaagtaagcttcctctgtcatttacggtccaaccgcaccctaccaacagaaaaacttctctaaaactgaatcgtcaaatactgctaacactaacttgaagaatgaaatatagtacaggcctactttgttgcaccatctgaa--gccttcctttgtatgtgatccctgcagTGTGTTTGTGTCAACTGCTAAAAGGCTGAGGGTTTTGAGGAGCTCGGAGCTTGCCAAAGGTTTGGTAGG---CACAAGGCCACCTCAG------------Mapped 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|4714667|gb|AU055784.1|AU055784EST: TATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAA AGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCT
genomic: TATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgc ... attcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGGTAAGACAAGCTAGACCACTTAAAGTCGTGTCCAAA
atctaaa putative branch site (score: 3)
tttttcctgttctcca putative PPT
atctaaattattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacactgccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcagAGTATTTGTCTCAACTGCTAAAAGGCTGAGGGTTCTAAGGAGTTCAGAGCTTTCCCATACCCTGGTAAGACAAGCTAGACCACTTAAAGTCGTGTCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT