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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcctgtcttttatttcattattgattacatcttgtattacttggttcaaggtttagaattgatgaagtaaagagtgctagtacatctttttaat...

Basic information

species Zea mays
transcript GRMZM2G139462_T06
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139462_T06 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 5'ss of exon 3
ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcctgtcttttatttcattattgattacatcttgtattacttggttcaaggtttagaattgatgaagtaaagagtgctagtacatctttttaat
|| || ||||| ||||||||||| |||||||||||||||| ||||||||||||||||  |   || |||| |||   |||||| |||  |     ||||  || || ||| || | | |  || |||| ||   |  |    ||| |   || |
ATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAGgtgtgccagtgcctttcattcttttattgcttatttacccgattaactgtttgaagattgaaattaaatcaagtgaaacataattaggcatgtacatagt
















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|74244525|gb|DT652439.1|DT652439
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|78076648|gb|DV505082.1|DV505082
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|76917142|gb|DV166699.1|DV166699
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATA
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATA
EST: gi|76286637|gb|DV026205.1|DV026205
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|211173537|gb|FL094957.1|FL094957
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|76013765|gb|DT940935.1|DT940935
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|33467006|gb|CF244055.1|CF244055
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|50335608|gb|CO530734.1|CO530734
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|50338057|gb|CO533183.1|CO533183
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|211173536|gb|FL094956.1|FL094956
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTT
EST: gi|84980665|gb|DW531014.1|DW531014
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|211175204|gb|FL094961.1|FL094961
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTG
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTT-GCTATTGTTGTTGGCGGTGGCAATATCTTCCGTG
EST: gi|211175207|gb|FL094964.1|FL094964
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGG
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGG
EST: gi|211175211|gb|FL094968.1|FL094968
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGG
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGG
EST: gi|211175203|gb|FL094960.1|FL094960
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|91056257|gb|EB166675.1|EB166675
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|50326142|gb|CO521268.1|CO521268
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|86466839|gb|DY233209.1|DY233209
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|78119797|gb|DV538181.1|DV538181
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|78106046|gb|DV524464.1|DV524464
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|211175212|gb|FL094969.1|FL094969
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTT
EST: gi|74235299|gb|DT643213.1|DT643213
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|71437591|gb|DR818641.1|DR818641
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|86468321|gb|DY234691.1|DY234691
EST:     CAATGGCTATTGCAAGAAAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|71766564|gb|DR964501.1|DR964501
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|211173532|gb|FL094952.1|FL094952
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGC
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGC
EST: gi|148960321|gb|EE153577.2|EE153577
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|76285330|gb|DV024898.1|DV024898
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|211173534|gb|FL094954.1|FL094954
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|50331445|gb|CO526571.1|CO526571
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|71433983|gb|DR815033.1|DR815033
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
EST: gi|76291661|gb|DV031229.1|DV031229
EST:     CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG                         GTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT
genomic: CAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCT

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: 41 (upstream exon), 46 (downstream exon)
Score: 67

ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 161

ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGG


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 17

ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGG


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 59

ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcct ... gcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAGgtgccctcctgtcttttatttcattattgattacatcttgtattacttggttcaaggtttagaattgatgaagtaaagagtgctagtacatctttttaat

- - - - - - -  GCAAGA
- - - - - - - -  AAGAGA
- - - - - - - - - - AGAAGT