Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgttcctgtacattgtgaattcaggagaaaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGCAGAGCCCCATCATGGAGTGAATGGTTGTATAATAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g10740.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G813363_T02 (Zea mays), 3'ss of exon 5
---------------------------------gtgagtgttcctgtacattgtgaattcaggagaaaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGCAGAGCCCCATCATGGAGTGAATGGTTGTATAATAAG
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gtgcgtatgttctcactctctttgcggtatgttctcacacttcattcagacttgtaacttgatacaaaatcactatcctatgttgagttaacaaggattttatactcttcaat------agACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAA
upper sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G813363_T03 (Zea mays), 3'ss of exon 5
-------gtgagtgttcctgtacattgtgaattcaggagaaaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGCAGAGCCCCATCATGGAGTGAATGGTTGTATAATAAG
| | ||| | | | | || | | |||||| || || || | ||| | || || | ||||| |||||||||||||||||||||||||||| |||||| ||||||||||||| |||| |||| || ||||| || ||| ||||||||||
gtatgttctcacacttcattcagacttgtaacttgatacaaaatcactatcctatgttgagttaacaaggattttatactcttcaat------agACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAA
upper sequence: LOC_Os05g10740.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G813363_T01 (Zea mays), 3'ss of exon 5
-------gtgagtgttcctgtacattgtgaattcaggagaaaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGCAGAGCCCCATCATGGAGTGAATGGTTGTATAATAAG-------------
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gtatgttctcacacttcattcagacttgtaacttgatacaaaatcactatcctatgttgagttaacaaggattttatactcttcaat------agACGAAATACCGGGAGAGGGTAATAGGATTGATGCTGGTTTCCCCTCTGTGCAAGTCCCCGTCGTGGAGCGAGTGGCTGTATAATAAAGTAACTTACATCTMapped 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|29643622|gb|CB648629.1|CB648629EST: TGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA ACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGC
genomic: TGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCAgtgagtgttc ... attgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGC
EST:
gi|33797484|gb|CF324602.1|CF324602EST: TGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCA ACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGC
genomic: TGATGTGCCTGGGTGTTACAGCTGGTGCCTATGTCCTCACTCTGTTTGCAgtgagtgttc ... attgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGCAGAGCCCCATCATGGAGTGAATGGTTGTATAATAAG
tgctaat putative branch site (score: 2)
ttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgttcctgtacattgtgaattcaggagaaaatcttactcttagactgtgctaatgacaatcttcattttctcaattgtcgcagACGAAATACCGGGAGAGGGTAATAGGCTTGATGTTGGTTTCCCCTCTATGCAGAGCCCCATCATGGAGTGAATGGTTGTATAATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA