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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatccccaattgctttagtacaatctatcgtgctaccgtgtggataatatagtctttaatcccgagagaaagagagcttggtgagagaaaaaaaagga...

Basic information

species Zea mays
transcript GRMZM2G039325_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 2
ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatccccaattgctttag--tacaatctatcgtgctaccgtgtg--------gataatatagtctttaatcccgagagaaagagagcttggtgagagaaaaaaaagga
|||||||||||||||| |||||||| ||||||||||||||||| || ||  |||||||||||||||||||||| ||||| |||||||||||  ||    ||||     |  | |   | || | ||  | ||        | | || || |  ||  ||| || |     |   | |    |  ||          
ACAAGGAGAGGGAGCTCGGGGAGGCGCAGACGGAGATACGCGCGCTACGGCTGTCGGAGAGGGCGCGGGAGAAGGCCGTGGAGGAGgtaattgccgtcagcttcgtcctggatttcgtggttcaacgatatgcttttcctgtttatttatttgtttttcctgaaatggcaatttcctttgcattga----------
















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|149084677|gb|EE174161.2|EE174161
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|211231947|gb|FL170987.1|FL170987
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAA-CTCAAGCTGAC
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGAC
EST: gi|71444483|gb|DR825533.1|DR825533
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|211453386|gb|FL460028.1|FL460028
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|211234007|gb|FL171000.1|FL171000
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAAACTCA-GCTGACAGAATC
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAA-CTCAAGCTGACAGAATC
EST: gi|149113193|gb|EE295942.2|EE295942
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|211415054|gb|FL462009.1|FL462009
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|148943243|gb|EC888304.2|EC888304
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|148967769|gb|EE019046.2|EE019046
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|76930993|gb|DV172583.1|DV172583
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|71444482|gb|DR825532.1|DR825532
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
EST: gi|71439208|gb|DR820258.1|DR820258
EST:     TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAG                         CTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT
genomic: TACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCT

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), 43 (downstream exon)
Score: 287

ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTTGAAAGCAAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 112

ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTTGAAAGCAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 156

ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTTGAAAGCAAA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 166

ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatcccca ... ttgatggcagCTTACAGATGAATTGGAGAAGATGGCTGAGAAACTCAAGCTGACAGAATCTCTCCTTGAAAGCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAGGAGAGGGAGCTTGGGGAGGCACAGACGGAGATACGCGCACTGCGCTTGTCGGAGAGGGCGCGGGAGAAAGCCGTCGAGGAGgtaatccccaattgctttagtacaatctatcgtgctaccgtgtggataatatagtctttaatcccgagagaaagagagcttggtgagagaaaaaaaagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaaa