Sequence
atgc intronic sequence ATGC exonic sequence...ttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g19510.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g19510.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G006507_T04 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------ttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
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gtatgttcactaccacatccacaaatttcattttaatatataaatagtccttgtttagtctgtatatttaactactagtgt--acctaatgtcggataattttgt---gtcctcgttgccactcatcctaattttactgccaatatttgtcagcagCAGCATGCCAAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAAC---
upper sequence: LOC_Os02g19510.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 2
------------------------------------ttgcccacttgtctagtaacaccaacca--agtgttctttttctt------tctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
| | | ||| ||| ||||| | | | || | | || ||| | | ||| ||||||| | || || || | || ||||||| ||||||||| |||||||| ||| |||||||||| ||||||||||| ||||| ||| |||| ||| |||||||| | |||||||||||||| || |||
gtatgttcactaccacatccacaaacttcataagcagttcttgttcagtctgtagatttaactgctagtgtacctaatgttgggcaattttatgtcctcggtgccactcatcgtaattttactgccaatttttgttattaacagCATGCCAAGATCGAATGAGGGAATGCGGCTCATATTTTCGGCAGTTGTAGGTGTCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATA
upper sequence: LOC_Os02g19510.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------ttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
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gtatgttcactaccacatccacaaatttcattttaatatataaatagtccttgtttagtctgtatatttaactactagtgt--acctaatgtcggataattttgt---gtcctcgttgccactcatcctaattttactgccaatatttgtcagcagcagCATGCCAAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAMapped 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|58686132|gb|CK074819.1|CK074819EST: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG CACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... tcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
atttaat putative branch site (score: 4)
acattgtaatttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcccacttgtctagtaacaccaaccaagtgttctttttctttctacggtgctcatggttgcacattgtaatttaattgtgaacattcatcatcaacagCACGCCAAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATA
-tgcccac
- - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - tgttctt
- - - - - - - - - - - - - - - - - - - - - - - - ggtgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca