Sequence
atgc intronic sequence ATGC exonic sequencegtgctatacttttgaatgagctccatattaatagtcttaactctgaagtaactcttctatggaggccttctcattgacccttcagtttaattaaacagAAAGAAGGACGGCAGCGTGGAACTTGGAGTGGAAAAAAGAATGACAATGATTATTACAAAATGATT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g14460.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G147500_T01 (Zea mays), 3'ss of exon 8
gtgctatacttttgaatgagctcca-tattaatagtcttaactctgaagtaactcttctatggaggccttctcattgacccttcagtttaattaaacagAAAGAAGGACGGCAGCGTGGAACTTGGAGTGGAAAAAAGAATGACAATGATTATTACAAAATGATT
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gtgatatgcctgtgaatcttcttgaatgtta--ggtcttaatactatattgttttgtttttgga-----tcttatttggtt----actgaacttatcagAAAGAAGGACGACAACGCGGAACATGGAATGGAAAAAAGAACGACAATGATTATTACAAAATGATT
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 8
----gtgctatacttttga--atgagctccatattaatagt--cttaactctgaagtaactcttctatggaggcc-ttctcattgacccttca-gtttaattaaacagAAAGAAGGACGGCAGCGTGGAACT--TGGAGTGGAAAAAAGAATGACAATGATTATTACAA--AATGATT
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aaaagaacgacaatgattattacaaaatgattgtaagcagtaacgcaattttgaaatgcagatctgattgaatttattctgatgtatattatgtattcagGTTGATGCATATGAAGTGAAGAAACAAGAGCTGATGCAAGAGAATGCAGATTTACGGGCACTGTTACGTTCAATGCAG
upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 8
gtgctatacttttgaatgagctccatattaatagtcttaactctgaagtaactcttctatggaggccttctcattgacccttcagtttaat-taaacagAAAGAAGGACGGCAGCGTGGAACTTGGAGTGGAAAAAAGAATGACAATGATTATTACAAAATGATT
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---------gtgtcagtctgccaattgcttgttctgagatttctgaatttttttggttgaaagcatttcataattggcctttgtgcttggtgtaaacagAAAGAAGGGCGACAACGTGGGACATGGAATGGAAAGAAGACTGACAATGATTTCTATAAAAAAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagtaactcttctatggaggccttctcattgacccttcagtttaattaaacagAAAGAAGGACGGCAGCGTGGAACTTGGAGTGGAAAAAAGAATGACAATGATTATTACAAAATGATT
ttcagtttaattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctatacttttgaatgagctccatattaatagtcttaactctgaagtaactcttctatggaggccttctcattgacccttcagtttaattaaacagAAAGAAGGACGGCAGCGTGGAACTTGGAGTGGAAAAAAGAATGACAATGATTATTACAAAATGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA