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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG

Basic information

species Zea mays
transcript GRMZM2G145595_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgc--------------acggagaattc---cagtggatacattaaccagacctatgctagggagc--ctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
        | | |  |   |||||||| | ||| |||||| |  ||  |              ||   | || |   || || ||||  ||  |||||  ||||||  |||    | ||||| |||||| |  ||||  || | |||   |  | ||||  |||||  ||||||||||| || |||||||| |||||||||||||||||||| || || || |||||||||||||| |||||||| ||||||||||| ||||||||||| |
--------gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaat--gatgagacatgaactctact--tttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 7
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgt----atccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
                                                          |  |  | || || |     |   |   |||||     |||     | | |      ||| | | |  | | || ||   |   || ||||    ||| |||| ||  | |||||||| ||||| ||  | ||||| ||||| || || ||||||||||||||||||||||| |||||||| ||||| || || || |
--------------------------------------------------------tcttgaccgtattcactcttatgcttttctctaggtgcattgttgttgttctttacttgtctcattgtttactaactatttttaagctgttttcatgcagTTGATATACAGACCTGACACTGGAGAGATATTGGGAGTCCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCACTAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatg---ctagggagcctg-tatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
                                                         |||  |    ||  | |  |  |||| |    ||||      || | | | |        | | | |  | | || |    |   || ||||    ||| |||| ||  | |||||||| ||||| || || ||||||||||| || || ||||||||||||||||||||||| |||||||| ||||| || ||  | |
--------------------------------------------------------cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 12
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
                                           | |||    ||    | |   |    ||||  |      |    |       |||| | ||   | | |   | |   || || || |  |||  || | |||   ||| |||| ||| | |||||||  ||||| || || |||||||||||||| || |||||||| || |||||||||||||| ||||| ||||| |||||  | |
-------------------------------------------tcatg---agacttgttctacgctctcattttctctggatgcatttacttctctgttttcacc-agcttgacattgctaattgtcgttttatg--ctttcttg---cagTTGATATATAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATTGCATTAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 12
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
                             ||  ||       ||  ||| |    | || |  ||| | |||| || |   || || |        | || |     | | |   | |   || || || |   | | || | |||   ||| |||| ||  | |||||||  ||||| || || |||||||||||||| || |||||||| || |||||||||||||| ||||| ||||| || ||  | |
-----------------------------gtcacaagacttgttc-tgcgctctcattttctttgggttcatttacta---ctctgtt--------tttacc-----agcttgacattactaattgtcgtt---tatgctttcttg---cagTTGATATACAGACCTGACAATGGAGAGATACTAGGAGTTCATATTTTTGGTTTGCATGCAGCAGATCTCATCCATGAAGCATCCAATGCAATAGCATTAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
                                              || |  ||  |  |||     |  | |||  | |  || | |  | |    ||      |  || |   ||  | |  |  |   |||    ||   |     |||||||| ||  | |||||||  || ||||| |||||||||||||| || || ||||||||||||||||| |||||||| |||||||| || |||||  | |
---------------------------------------------gtgaagagaagaa-ccaaaaattgaaataaaaaaagata-gtt--gtatatagttctggagtgacttgcgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 12
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgta-ctattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
                                                 |     || | |  |     ||||    |        | |   |||   ||  | |   || |||    ||    || | || | | |  |||||||    ||| |||| ||  | |||||||  ||||| ||||||||||| || || || || ||||||||||| || || |||||||| ||||| ||||| || || || |
-------------------------------------------------attagaaagtgcttttagcccattttaaaattactcccaaataagctcttagtctttctacttctgccatt----tgccaattcttctgtctattttcatccagTTGATATACAGACCTGACAATGGAGAGATTCTTGGAGTGCACATCTTTGGGTTGCATGCTGCAGACCTTATCCATGAAGCATCCAATGCTATAGCACTAG

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|211470347|gb|FL451278.1|FL451278
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|20512800|gb|BQ279999.1|BQ279999
EST:     AGGGTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|13249875|gb|BG360780.1|BG360780
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|211093993|gb|FL455618.1|FL455618
EST:     GGCTAACACAAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: GGCTAACAC-AAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|211470346|gb|FL451277.1|FL451277
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|16378429|gb|BI992442.1|BI992442
EST:     AGGCTANCACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|6865111|gb|AW360461.1|AW360461
EST:     AGGAGATGGCCTTGCTAAG                         ATGATTTATCGCCCTGACNCCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|13249874|gb|BG360779.1|BG360779
EST:     AGGCTAACGCAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|32830615|gb|CD970293.1|CD970293
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|26456706|gb|CA828289.1|CA828289
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|32830552|gb|CD970230.1|CD970230
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|32831600|gb|CD971278.1|CD971278
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
EST: gi|211093992|gb|FL455617.1|FL455617
EST:     AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAG                         ATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC
genomic: AGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGC

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: 83

GAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

GAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

GAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAGATGGACTTGCTAAGgtagtaatgc ... tttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG
             ctctaaa  putative branch site (score: 102)
                                            ttttgcctc  putative PPT
                taaatttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatgctagggagcctgtatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT