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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatccttttccccctatgtacatataaaccatacattatatgatggttcaaattttatcatactcattctgttaaatcctttactatttag

Basic information

species Zea mays
transcript GRMZM2G412888_T01
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g41730.2 (Oryza sativa), 5'ss of exon 2
GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcct---tttccccctatgtaca-tataaaccatacattatatgat-ggttcaaattttatcatact-cattctgttaaat-cctttactatttag--
||||||| |||||||||||||||||||||||||||||||||||    ||  |  |||  ||| |  ||   ||||   || | |  || | | |    ||     |  ||||| || ||| |||||||| || |   
GTCCAACTATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctgaaattttctatatagacactgaaagttataccacattttacaggcttatagacgatggggttatattcttttgaattcctttactcttaatag

upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G05930.1 (Glycine max), 5'ss of exon 2
GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatccttttccccctatgtacatataaaccata--cattatatgatgg----ttcaaattttatcatactcattctgtt----aaatcctttactatttag------
||||||||||| |||| || |||||||||||||| ||||||||  |         |||  ||||    |   ||||||  | |      ||     || |  |   ||| |||| |    ||  |||| |||  | |       
GTCCAACCATTTTGTTTTTTCAAGAAAATGCTGGAAgtatcctgattgtagatattacgcataagttgtgatcattattagttcacatatttttgcttgagtaggttcaatctgcttttaaaggccttgactgctgacttttag

upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv11s0016g01490.t01 (Vitis vinifera), 5'ss of exon 2
GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatccttttcccc-ctatgtacatataa--accat--acattatatg--atggttcaaattttatcatactca-ttctgttaaatcctttactatttag-------------------------------------------
||||||| |||||||| |||||||||||||| || |||||||||||  |  | |  ||  ||| |  | |||  | ||||| ||  ||  ||        || | | |   || ||||      |   || | |                                             
GTCCAACAATTCTGTTTTTCCAAGAAAATGCAGGAAgtatccttttatcagcaacatagttatgatcatcattaatattatttgttattatttgggaacaataacattaggttatgtttgcatttcatctttgtgattgggttcagcattttcagagggcctttactagtcaaatacag

upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S104_135V6.2 (Physcomitrella patens), 5'ss of exon 3
GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatccttttccccctatgtacatataaaccatacatta-tatgatggttcaaattttat-catactcattctgttaaatcctttactatttag----------
| |||||  | || |||||||||||||||||||||||||||||   ||    |  ||  |    ||   |  ||  | |  |  |    ||   || ||||    || ||||        || ||||| |          
GGCCAACATTCCTTTTCTTCCAAGAAAATGCTGGCAgtatcct---ccgatgaaatatttcgtcacttgattttggtgtctttatatgcatggaattcataaatgttatgttgtgatgagta-tatttggggaggagttt

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|26557244|gb|CA829479.1|CA829479
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|71425140|gb|DR806559.1|DR806559
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|76018058|gb|DT945228.1|DT945228
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|71430933|gb|DR811983.1|DR811983
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|211463531|gb|FL255623.1|FL255623
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|71427907|gb|DR808957.1|DR808957
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|89250823|gb|DY622609.1|DY622609
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|29129758|gb|CB380462.1|CB380462
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|149008856|gb|EE041069.2|EE041069
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|71448310|gb|DR829360.1|DR829360
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|71316274|gb|DR794814.1|DR794814
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|89253014|gb|DY624800.1|DY624800
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|148933213|gb|EC876864.2|EC876864
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|148939301|gb|EC883808.2|EC883808
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|31664225|gb|CD572950.1|CD572950
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAG-
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|30705302|gb|CD058738.1|CD058738
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|76293689|gb|DV033257.1|DV033257
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|89252853|gb|DY624639.1|DY624639
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGGCTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|67011215|gb|CO439964.1|CO439964
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|8103365|gb|AW928006.1|AW928006
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|88750379|gb|DY534520.1|DY534520
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAGTGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|91055111|gb|EB165529.1|EB165529
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|88752413|gb|DY536554.1|DY536554
EST:     GTCCAACCATTCTGTTCTTCCA-GAAAATGCTGGCA                         ACATCGCTCACCGTTTGGATTTTGTTCGACTAATGATGCAGCG
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCG
EST: gi|67041292|gb|CO467547.1|CO467547
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|29576736|gb|CB616848.1|CB616848
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|148947394|gb|EC892802.2|EC892802
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|149014757|gb|EE044444.2|EE044444
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|71437275|gb|DR818325.1|DR818325
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
EST: gi|148933571|gb|EC877438.2|EC877438
EST:     GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA                         ACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT
genomic: GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGT

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: 36 (upstream exon), 48 (downstream exon)
Score: 195

GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGTGCAATGTTTTTATGCTTTCTTATAGAGG


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 240

GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGTGCAATGTTTTTATGCTTTCTTATAGAGG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 239

GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGTGCAATGTTTTTATGCTTTCTTATAGAGG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 240

GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatcctttt ... tactatttagACATCGCTCACCGTTTGGAATTTGTTCGACTAATGATGCAGCGACTACAGTGCAATGTTTTTATGCTTTCTTATAGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCAgtatccttttccccctatgtacatataaaccatacattatatgatggttcaaattttatcatactcattctgttaaatcctttactatttag

- - - - - - - - - -  AAGAAA
- - - - - - - - - - - - -  ATGCTG