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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttctacctgtgaatttctgcagttatttaaaaatgctctggaccctgtgatgacctctcactattatttttatctatgtttctgcagtttagg...

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 5
ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgcttt-ctacctgtgaatttctgcagttatttaaaaatgctctggaccctgtgatgacctctcactattatttttatctatgtttctgcagtttagg--
|||||||||||||| ||||||||||| || |||||| ||||||| ||||| ||||||||||| || || ||||||||||||||||||||||| || ||| ||| |     |||| | |  || ||||    | |  |  |   ||| |   | |   || || |  |  |   || |   | || | |     
ATTGCAGCATACCCTAAGGCAACTGCAGTCCTTGTACGGAACCATGGAATTTATGTATGGGGTGATTCCTGGATCAATGCCAAGACACAGgtatgtttttctaacctctcatttttact-ttgtttatttcttcattttagattgtcagctctttcaacaatcaaat--agtaatctccttacactatgccct

upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S1_661V6.3 (Physcomitrella patens), 5'ss of exon 5
ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttctacctgtgaatttctgcagttatttaaaaatgctctggaccctgtgatgacctctcactatta----tttttatctatgtttctgcagtttagg
|| | ||| || || |||||||||||||| || || ||||||||||| |||||| | ||||| || ||||||||||  || || || ||||||   |    |  |  |   | |     |  ||||    ||   || | | |  | ||     | |||  ||    |   |||| ||  |       ||| | 
ATGGAAGCGTATCCTAAGGCAACTGCTGTCCTCGTGAGGAACCACGGCATATATATCTGGGGTGATTCTTGGATCAGCGCGAAAACCCAGgtgccatgaagaatttgg---tcccattatggtttatttttgaattgaaacataaggtgtttgattacttctaagattgcctatcaatagtagaaggatttgg-
















Mapped 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|76289240|gb|DV028808.1|DV028808
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|211266802|gb|FK955969.1|FK955969
EST:     CGGAAT-T-TGTATTTGGGGGGAGAATCTGGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATC
genomic: CGGAATATATGTAT--GGGGGGAG--TCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATC
EST: gi|26457260|gb|CA828843.1|CA828843
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|32862805|gb|CF002487.1|CF002487
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|21390180|gb|BQ528229.1|BQ528229
EST:     TATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: TATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|60351211|gb|DN218184.1|DN218184
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|148957566|gb|EC903663.2|EC903663
EST:     ACCACGGAATATATGTATGGNGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|31355926|gb|CD440283.1|CD440283
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
EST: gi|12967932|gb|BG264879.1|BG264879
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATC
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATC
EST: gi|149079628|gb|EE168621.2|EE168621
EST:     CCACGGAATATATGTATGGGGGGAGTCTTGGGATCA-TGCCAAGACACAG                         GCTGAATGCTACCATTAT
genomic: CCACGGAATATATGTATGGGGGGAGTCTTGG-ATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTAT
EST: gi|149079514|gb|EE168492.2|EE168492
EST:     ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTT
genomic: ACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTT
EST: gi|109179163|gb|EC379844.1|EC379844
EST:     CCACGGCAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAG                         GCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA
genomic: CCACGG-AATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 214

ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTAGGTATTGATTGGACAACCCCTGAACATGGTTCAATAAACAATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTAGGTATTGATTGGACAACCCCTGAACATGGTTCAATAAACAATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 417

ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTAGGTATTGATTGGACAACCCCTGAACATGGTTCAATAAACAATCCAAGGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 143

ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttc ... tgcatttcagGCTGAATGCTACCATTATCTTTTAGATGCTTGCATCAAGCTCTATCAGCTAGGTATTGATTGGACAACCCCTGAACATGGTTCAATAAACAATCCAAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCAGCATACCCAAAGGCAACTGCTGTGCTTGTAAGGAACCACGGAATATATGTATGGGGGGAGTCTTGGATCAATGCCAAGACACAGgtgtgctttctacctgtgaatttctgcagttatttaaaaatgctctggaccctgtgatgacctctcactattatttttatctatgtttctgcagtttagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctcac