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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagttatatgcatgcttggaaaattcgtagcttgatttctgtctttggcaactctgaccccaaaagcatgctttgcgagagcagtcaacaaatac...

Basic information

species Zea mays
transcript GRMZM2G101874_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101874_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 3
AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagttatatgcat-gcttggaaaattcgtagcttgatttctgtctttggcaactctgaccccaaaagcatgctttgcgaga-gcagtcaacaaatac
 ||  |||||||||||||||| |||||||||||||||||||| ||||| || || || || ||| | |||||||| ||||| || || || |||||||||||||||    ||   |||  | | ||| | || |   ||   | |   | |  |   ||| |      | |    |   ||| ||  |||    ||   |  
CACCGACTCTAGGGATCTCCTTATCCAGGCGCTGGATGACTCGAAGATTGAGCTGGCCAGACTTTTATCTGCTCTAGGAGAGAAGGCCATAGCAAGAACTgtaagtgagcattatcatcacattgaatagtcatttgttcgatgcaa-cgtgagtggctcagcggaggacaattggtggtgcaagttgcaacttacttgtc-
















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|211437198|gb|FL306605.1|FL306605
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACCACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|148932084|gb|EC875451.2|EC875451
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|148946917|gb|EC892199.2|EC892199
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|26456561|gb|CA828144.1|CA828144
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|29168001|gb|CB411261.1|CB411261
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|149058039|gb|EE156723.2|EE156723
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|31558097|gb|CD527309.1|CD527309
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|30087270|gb|CB885478.1|CB885478
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211137588|gb|FL389534.1|FL389534
EST:     AACTTCCTAGGCCTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTAAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211262089|gb|FL418798.1|FL418798
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211374013|gb|FL281466.1|FL281466
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCA
EST: gi|211511641|gb|FL407272.1|FL407272
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211189068|gb|FL364427.1|FL364427
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211291088|gb|FL325931.1|FL325931
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCC
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGG-ACAATCAAGCAGCAGCTAGCTGCTATAGCGCC
EST: gi|211121781|gb|FL425238.1|FL425238
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAAGACA-CAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCC
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAA-GACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCC
EST: gi|211197583|gb|FL428825.1|FL428825
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAANAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211194870|gb|FL416650.1|FL416650
EST:     AACTTCCTAGGCTTCTTTCTGCTCTCAGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|211211707|gb|FL374153.1|FL374153
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCCTGAGA-GACAACAGGGACAATCAAGCA-CAGCT
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCC-TGAGAAGACAACAGGGACAATCAAGCAGCAGCT
EST: gi|211353641|gb|FL411984.1|FL411984
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
EST: gi|91875287|gb|EB405244.1|EB405244
EST:     AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACT                         CCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA
genomic: AACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 378

AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCAACACTTGAGCAGTTGACTAAACAGAAAAATGAAAGAAAAAGAGAGTTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 50

AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCAACACTTGAGCAGTTGACTAAACAGAAAAATGAAAGAAAAAGAGAGTTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 58

AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCAACACTTGAGCAGTTGACTAAACAGAAAAATGAAAGAAAAAGAGAGTTTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 62

AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagtt ... atccgtgcagCCTGAGAAGACAACAGGGACAATCAAGCAGCAGCTAGCTGCTATAGCGCCAACACTTGAGCAGTTGACTAAACAGAAAAATGAAAGAAAAAGAGAGTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTAACTCTAGGGATCTCCTGATCCAGGCGCTGGATGACTCAAAGATAGAACTTGCTAGGCTTCTTTCTGCTCTCGGAGAAAAAGCTATTGCAAGAACTgtaagtagttatatgcatgcttggaaaattcgtagcttgatttctgtctttggcaactctgaccccaaaagcatgctttgcgagagcagtcaacaaatac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaata