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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtataggaagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG

Basic information

species Zea mays
transcript GRMZM2G019358_T06
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 14
gtatgtataggaagcacttcatcctgatattc-caattcacaatgtgctctttcttcccccaaaa-------------atgattttaacatt--cttcaaacatctt-------agGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG
||||||| ||| |||| ||  |  |    |||  ||    | | |   |  ||||||| ||| ||             || | ||| | ||    |||    || ||       ||||||||||||||||||||||| ||||    |||||||| |||||||||||||| ||| |||| || |  ||||| || |||
gtatgtagaggcagcatttgtttgttgccttcataagatgccacgccattcttcttcctccataagatcaaataaagcatcagtttcatataagtttcctgtattttttttttcagGGAAAGATATCAAGGGAAGAAATTGCTTTCATTTGTGTTGCAGCTCTGGCAAGTCCAAATGCAGTAGAGAAAACCTTTGAG
















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|32934374|gb|CF039186.1|CF039186
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGCCAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|13562283|gb|BG550503.1|BG550503
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|7304470|gb|AW600409.1|AW600409
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|13125927|gb|BG316602.1|BG316602
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211503640|gb|FL133352.1|FL133352
EST:     GGTACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGAACA-CATCACA                         GGGAAGAT-TCCAAGGGGAGGAGTTGCCCCGTATTTGGTGTAGCAGCTCTG
genomic: GGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGA-CAACATCACAgtatgtatag ... aacatcttagGGAAAGATATC-AAGGGAAGAAGTTGCCC-GTATTTG-TGTAGCAGCTCTG
EST: gi|16377470|gb|BI991944.1|BI991944
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211503639|gb|FL133351.1|FL133351
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211501308|gb|FL133349.1|FL133349
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAAGT-GCCCGTATTTGTGTAGCAGCTCTGGC
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAA-GTTGCCCGTATTTGTGTAGCAGCTCTGGC
EST: gi|60352340|gb|DN219313.1|DN219313
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211501307|gb|FL133348.1|FL133348
EST:     AGGAATCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|7216720|gb|AW562842.1|AW562842
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|12968100|gb|BG265047.1|BG265047
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|71760712|gb|DR958649.1|DR958649
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|16378431|gb|BI992443.1|BI992443
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211357416|gb|FL471654.1|FL471654
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|148936819|gb|EC880960.2|EC880960
EST:     AGGAACCAGCTGGAGCCGATTTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGTTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|12967873|gb|BG264820.1|BG264820
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211503638|gb|FL133350.1|FL133350
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA

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: 102

TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 14

TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 129

TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG
                              ttttaac  putative branch site (score: 129)
                      aaaaatgattttaaca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtataggaagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG