Sequence
atgc intronic sequence ATGC exonic sequence...gaattatatatttttgtaccatttgatttggattcgttggttataaatcatgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
Basic information
species | Oryza sativa |
transcript | 13114.m00153 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 9
-----------------gaattatatatttt-tgtaccatttgatttggattcgttggttataaatcatgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
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ttagttaagtttcaaatatgatgtgtgtcttatgtgccatgtgacccaggttagtcagtgatata-catgaaaactttaa---------------gttatatctatatttg--tgtagGCATCACGACATTGGTGGGTGGTGGAACCGGACCAGCACATGGAACTTGTGCCACAACTTGCACTCCAGCACCATCTCAATTGAAATTAATGTTGCAGTC
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G060656_T01 (Zea mays), 3'ss of exon 3
-gaattatatatttt-tgtaccatttgatttggattcgttg-gttataaatca-tgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
| ||| | | | | | || || | | || | | | | | || | | | || ||| || |||| || |||| | |||||||||| ||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| | |||||||||| ||||| ||||| | |||||
ttagttaagtttcaaatatgatgtgtgtcttatgtgccatgtgacccaggttagtcagtgatataaatg--aaaactttaagttatatcaatatttg--tgtagGCATCACGACATTAGTGGGTGGTGGAACCGGACCAGCACATGGAACTTGTGCCACAACTTGCACTCTAGCACCATCTCAATTGAAATTAATGTTGCAGTC
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 10
-------gaattatatatttttgtaccatttgatttggattcgttggttataaatcatgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
|| | || | | ||| || | | | || || | || | | | || || | |||| || || | || |||||| ||||||||||| |||||||| ||||| |||||||| ||||||| |||| |||||||| || || ||||| ||| |||||| | |||||||| ||
gcattgaaaaccagatttatcattacttatttctctagcatccttcttgatccaa-actactcattggattt------tattcagtccttttctgtattgtatatagGTATCACAACATTAGTGGGAGGAGGAACAGGACCAGCTGATGGAACACGTGCTACAACTTGTACACCAGCACCAAATCAGATGAAATTGATGCTACAATC
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 9
-gaattatatatttttgtaccatttgatttggattcgttggt-tataaatcatgagaagtttgactgc-taaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
|| | | | | | || | | |||| || || | ||||| | | | || ||| || | ||| | |||||||||||||||| |||||||| ||||| ||||| | |||||| | ||||||||||| || || |||||||||| |||||||||||||| || ||
ctctcccctcatctccttttccccagggcagatatcatcagcctatatatgcagatgaatttgatggagtttaacgagtccttatttac---tttgtatgtagGCATCACAACATTAGTGGGAGGGGGAACCGGACCGACTGCTGGAACACGCGCCACAACTTGTACACCAGCACCATCTCAGATGAAACTAATGCTGCAATC
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 9
gaattatatatttttgtaccatttgatttggattcgt-tggttataaatcatgagaagtttgactgctaaagtatttcgt-tacttccgca-tttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
||| || || | ||| | ||| | | | ||| | | | | || | ||| | | | ||| | | ||| | |||||||||||||||| |||||||||||||| ||||| | |||||| ||||||||||||| || || |||||||||| |||||||||||||| || ||
--cttacat-ttctcacctcatctccttttccccagggtagatatcagcgtaggcagatgaatttgatggagtttaatgagtccttttgtactttgtatgtagGCATCACAACATTAGTGGGAGGTGGAACCGGACCGACTGCTGGAACACGTGCCACAACTTGTACACCAGCACCATCTCAGATGAAACTAATGCTGCAATC
upper sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 9
----gaat-tatatatttttgtaccatttgatttggattcgttggttataaatcatgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
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agcagaatctggatgatatggtgg-atcatttttcattgtgctggtta--aaccattttcccttt--ttatcatcttcattttctttttccataaatatatgtagGCATCACAACATTAGTGGGCGGTGGAACGGGACCTGCTGATGGAACTCGTGCAACTACTTGTACGCCAGCAGCCTCACATATGAAATTTATGCTGCAATCMapped 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|29616662|gb|CB621674.1|CB621674EST: CCATGTTCACTTCATATGCCCTCAATTGGCAGAAGAGGCAATTGCAAGTG GCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTG
genomic: CCATGTTCACTTCATATGCCCTCAGTTGGCAGAAGAGGCAATTGCAAGTGgttaggctcc ... ttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcatgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
tgctaaa putative branch site (score: 2)
tttactt putative PPT
atttacttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaattatatatttttgtaccatttgatttggattcgttggttataaatcatgagaagtttgactgctaaagtatttcgttacttccgcatttacttatagGCATCACAACATTGGTGGGAGGTGGAACTGGACCAGCACATGGAACTTGTGCCACAACTTGCACCCCTTCACCATCTCACATGAAACTAATGCTACAGTC
- - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc