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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtattacttctttcatagtatctacactaaatcacaaaagagagggatagttttcatccttaggggctactttcctatggtctcaagaagaagaaa...

Basic information

species Zea mays
transcript GRMZM2G152686_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 2
ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtattacttctttcatagtatctacactaaatcacaaaagagagggatagttttcatccttaggggctactttccta----tggtctcaagaagaagaaa
||||||||||||||||||||||||||||||||||||  | |||||||| || |||||   |      || || ||||||||||| ||||||||||| ||||| ||||||| |||||| |  || | |  |||  |    |   | |    | |||  ||||||| ||   || || |  |     | |||| |   |||  |  
ACATGGAGACCATGCATCACACCAGAAAGTTATTGACTTAGTAAAGGAATATAATGCTCAAACAAAGGATAACGTGATTGCTATTATGCTTGACACGAAGgtcagtattatttctttga--gtttttgtactctaatgtatgggcggttcacagtaatcatcctaagaacctgctatatttgtgttagtcttacacagagta--

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G28980.1 (Glycine max), 5'ss of exon 2
ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagt-attacttctttcatagtatctacactaaatcacaaa-----agagagggatagttttcatccttaggggctactttcctatggtctcaagaagaagaaa
 ||||| |||||||| || || ||||||||||||||  |||| |||||||| ||||| || ||||  |||||||||||||| ||||||||||||||||||||| || | | ||||  ||| |   | |    |   |  |        ||| ||||||  |  |  || |    |  | ||||   |   | |      |      
TCATGGGGACCATGCTTCTCATCAGAAAGTTATTGACTTGGTTAAGGAGTATAATGCTTCTCATGAAGACAATGTGATTGCAATCATGCTTGACACAAAGgttggttagttcttcgctcaaacattttgttttccttttcgtgtttttagacagggatc-tgctgttcatgtatgtttgctttgtcacaatgttgtattgg-----

upper sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G23150.1 (Glycine max), 5'ss of exon 2
ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagt-attacttctttcatagtatctacactaaatcacaaaagagagggatagttttcatccttag---gggctactttcctatggtctcaagaagaagaaa-
 |||||||||||||| || || ||||||||||||||  |||| ||||| || ||||| || ||||  |||||||||||||| ||||||||||||||||||||| || | | ||||  ||| |  |  |    |   |             | |  ||||  |  || |   |||||   || || | || |         | || 
TCATGGAGACCATGCTTCTCATCAGAAAGTTATTGACTTGGTTAAGGAATATAATGCTTCTCATGGAGACAATGTGATTGCAATCATGCTTGACACAAAGgttggttagttcttcgctcaaacaacttgttttcctttttgtttt-----gtttttttttttttttggacagggctgtgttgctcttgtatatttgctttgtaac

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|211274089|gb|FL097603.1|FL097603
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|211275907|gb|FL097618.1|FL097618
EST:     ACNATGCATCACATGCTGACNATGTGATTGCTATCATGCTTGACACAAAG                         G-ACCCAGA-GTTCGAAGTGGAGA
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACC-AGAAGTTCGAAGTGGAGA
EST: gi|148961971|gb|EE012768.2|EE012768
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|148957677|gb|EC903791.2|EC903791
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|211275899|gb|FL097610.1|FL097610
EST:     CAATGCATTCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCA
genomic: CAATGCAT-CACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCA
EST: gi|211277710|gb|FL097626.1|FL097626
EST:     ACAATGCATCACATGCTGACAATGNGATTGCTATCATGCTTGACACAAAG                         GGGACCAGAAAGTTCGAAAGTGGAGATTTGCCTCAACCGATATTTTCTGGA
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGG-ACCAGAA-GTTCGAA-GTGGAGATTTGCCTCAACCGATATTT-CTGGA
EST: gi|211275905|gb|FL097616.1|FL097616
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|211275906|gb|FL097617.1|FL097617
EST:     ACAATGCATCACATGCTGACNATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGAT
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGAT
EST: gi|148934386|gb|EC878416.2|EC878416
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|5296084|gb|AI782959.1|AI782959
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|211275912|gb|FL097623.1|FL097623
EST:     ACNATGCATCACATGCTGACNATGNGATTGCTATCATGCTTGACACCAAG                         GGACCAGAAGTTCGAAGTGGAGA
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGA
EST: gi|71426208|gb|DR807258.1|DR807258
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|211279516|gb|FL097639.1|FL097639
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATT
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATT
EST: gi|67041095|gb|CO467350.1|CO467350
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTNCA-CCGATATTTCTGGAAAG
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCT-CAACCGATATTTCTGGAAAG
EST: gi|211274093|gb|FL097607.1|FL097607
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTTGCCTCA-CCGATATTTCTGGAAAG
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTT-GCCTCAACCGATATTTCTGGAAAG
EST: gi|211274094|gb|FL097608.1|FL097608
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGGACCAGAAAGTTCGAAAGTGGAGATTTGCCT
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGG-ACCAGAA-GTTCGAA-GTGGAGATTTGCCT
EST: gi|211277719|gb|FL097635.1|FL097635
EST:     ACAATGCATCACAGGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGT-CGAAGTGGAGATTTGCCTCA-CCGATATTTCTGGGAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
EST: gi|148974537|gb|EE025324.2|EE025324
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCCGATATTTCTGGAAAG
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACC-GATATTTCTGGAAAG
EST: gi|67025561|gb|CO454310.1|CO454310
EST:     ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAG                         GGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC
genomic: ACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGC

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), 49 (downstream exon)
Score: 154

ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGCGGACAAGAATTTACTTTTACAATCAAAAGGGGAGTTGGGACTGATACGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 136

ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGCGGACAAGAATTTACTTTTACAATCAAAAGGGGAGTTGGGACTGATACGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGCGGACAAGAATTTACTTTTACAATCAAAAGGGGAGTTGGGACTGATACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339

ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtatta ... tacaattcagGGACCAGAAGTTCGAAGTGGAGATTTGCCTCAACCGATATTTCTGGAAAGCGGACAAGAATTTACTTTTACAATCAAAAGGGGAGTTGGGACTGATACGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGGAGACCATGCATCACACCAGAAAGTTATTGATCTGGTAAAGGAGTACAATGCATCACATGCTGACAATGTGATTGCTATCATGCTTGACACAAAGgttagtattacttctttcatagtatctacactaaatcacaaaagagagggatagttttcatccttaggggctactttcctatggtctcaagaagaagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaagaa