Sequence
atgc intronic sequence ATGC exonic sequence...gttattcctttatttataacatctgccaagttaatttcaggcattcttggtttgtttttggatgattccttatgtcttgcatccatttctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g42330.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 2
gttattcctttatttataacatct-gccaagttaatttcaggcattc--ttggtttgtttt----tggatgattcctt----atgtcttgcatccatt--tctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG
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-------------gtatgccaacttgccaagttggttttgattatttatctgatttgtctacatgtggatagctccctctctatttcttacatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 2
gttattcctttatttataacatctgccaagttaatttcaggcat-tcttggtttgtttttggatgattccttatgtcttgcatccatt--tctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG
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gccaa--cttggcaagttggttttgatta-tttatctgatttgtgtatcagtgtatatgtggatggcaccctatatcttatatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGG
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174730_T02 (Zea mays), 3'ss of exon 2
gttattcctttatttataacatctgccaagttaatttcaggcat-tcttggtttgtttttggatgattccttatgtcttgcatccatt--tctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG-------------------------------------
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gccaa--cttggcaagttggttttgatta-tttatctgatttgtgtatcagtgtatatgtggatggcaccctatatcttatatctgttgatgttgatatttagGATCTGAAGAAAAAGGAGAAAGAACTCCAGGCTATGGAGGCTGAGCTAAACAAAAGAGAACGGGTGTGTTGGCTTTCAGTCTTTCTGCTCCTTTTGCCAG
upper sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 3
--------------------------------gttattcctttatttataacatctgccaagttaatttcaggcattcttggtttgtttttggatgattccttatgtcttgcatccatttctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG
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gtctgtataataaaaattgaggctgttgaaatcccaaacctctttttttttcatatat-aaatgcattacatgtattgttg---tgaaaattgattgtgggttttctaat-tatgatttgttttaacattagGATTTGAAAAAGAAGGAGAAAGAACTCCAAGCCAAGGAGAATGAATTGAGAAAAAGGGAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtttgtttttggatgattccttatgtcttgcatccatttctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG
tccatttcttt CT-rich tract
atttctttgaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattcctttatttataacatctgccaagttaatttcaggcattcttggtttgtttttggatgattccttatgtcttgcatccatttctttgaatttagGATTTGAAGAAAAAGGAGAAAGAACTCCAGGCAATGGAAGCTGAACTAAACAAAAGAGAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - - -ggcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatcc