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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatattggtctgtcaaccagtttaaatggccttttatttgtgtcaaattcttattgtttgtctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 19
------gttcatattggtctgtca--accagtttaaatgg-ccttttatttgtgtcaa-attcttattgtttgt----ctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
       || | |     ||  ||   |   ||| | ||| || | |  ||||| |||  |||||||||||| |    ||   ||| | ||||||||||| | || ||||||||||| ||||||||||| ||||| ||||||||||| || || |||||
gtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 19
gttcatattggtctgtcaaccagtttaaatggcctttt---atttgtgtcaaattctta--ttgtttgtctgt-acttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
  | |  ||  | | ||||| |   ||  |   || ||   |||||   |   || | |  |  |||  || | |||    ||||  |||| ||||| ||||| |||||||| || ||||||||||| |||||||||||||| || || ||
-gtgagtttattttatcaactaccatagttcttctcttctgatttgacgcggtttgtgagatgatttcactttgactgagcagGCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTCAACCAGCTATACAGTTCCATCAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 19
gttcatattggtctgtcaaccagtttaaatggcctttt---atttgtgtcaaattctta--ttgtttgtctgtacttgt-tagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
  | |  ||  | | ||||| |   ||  |   || ||   |||||       || | |  |  |||  || |  |||   ||||  |||| ||||| ||||| |||||||| || ||||||||||| |||||||||||||| ||  | ||
-gtgagtttattttatcaactaccatagttcttctcttctgatttgatgtggtttgtgagatcatttcactttggttgagcagGCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTGAACCAGCTATACAGTTCCGTCAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 19
--------------------------------------gttcatattggtctgtcaaccagtttaaatggccttttatt-tgtgtcaaattcttattgtttgtctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
                                       ||| | |   ||| |   |   |  | |    | |   |  ||   | ||    | |   ||| |  |       ||||| |||| ||||||||||| ||||||||||||||||||||||| || || || ||||| || |||||
gtgaactatccttatgcaaaagctcgaaagctctaaattttcttgtccatctcttttctcttacagagattcctcggtcatgctactaagcgatgtgaattgaccatg---aacagGCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
--------------gttcatattggtctgtcaa--ccagtttaaatggccttttatttgtgtcaaattc-ttattgtttgtctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
               ||| | |   |   | ||  ||  |   |||  |  |||   |   || |   | ||| |   | | ||   |    ||||| |||| || ||||||||||||||| | |||||||||||||| || |||||||||||||| || ||
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
gttcatattggtctgtcaa--ccagtttaaatggccttttatttg-----tgtcaaattctt-attgtttgtctg--tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
||    | | |||  | ||  |   |||      | ||  || ||     |  ||||| ||| | | | ||   |  |  |||  ||||  |||| ||||| ||||| |||||||| |||||||||||||| || ||| | |||||||| || ||
gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 18
-------------------gtt-catattggtctgtcaaccagtttaaatggccttttatttgtgtcaaattctt--attgttt--gtctgtacttgtt--agGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
                   |||  || | ||  |||     |  | || ||   |||  ||  ||| | | |||   |  | ||   |   | | ||||  ||||  |||| ||||||||||| |||| ||||||||| | |||||||||||| || || ||||| || ||
cccaggctaagctttacaagttgtatgtagggttgttggtga--tcaagtg-tttttctttgatgttatactctctaacaggttcaattctttcatgttccagGCAGTTGTCCTTTGTCAAGTAGAGAGAGCAAAGGATGCCATGCTTAACCAACTTTATAGCTCTATCAG

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|12046697|gb|BF728836.1|BF728836
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCA
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCA
EST: gi|78543683|gb|DV621181.1|DV621181
EST:     CGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: CGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|19821990|gb|BQ048014.1|BQ048014
EST:     GTGGTTATGTCGAGGCTGCTATGAATAGTCTGGCAGCAAATGTTCCTAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|24768960|gb|CA404089.1|CA404089
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|78180891|gb|DV551264.1|DV551264
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|71773970|gb|DR971858.1|DR971858
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|26455909|gb|CA827492.1|CA827492
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|166637116|gb|EG319162.1|EG319162
EST:     TCTGGCAGCAAATGTTACCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCA
genomic: TCTGGCAGCAAATGTT-CCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCA
EST: gi|31355296|gb|CD439653.1|CD439653
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|56382295|gb|CV984964.1|CV984964
EST:     GTGGTTATGTCGAGGCTGTTTTGAATNGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|31357385|gb|CD441742.1|CD441742
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|22491320|gb|BU051243.1|BU051243
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|149096022|gb|EE181696.2|EE181696
EST:     TGGTTATGTCGAGGCTG-TTTGAAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TGGTTATGTCGAGGCTGTTTTG-AATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|32940832|gb|CF045651.1|CF045651
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|67026008|gb|CO454757.1|CO454757
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|87151847|gb|DY396636.1|DY396636
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|32857965|gb|CD997646.1|CD997646
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGGGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211132361|gb|FK982428.1|FK982428
EST:     GTGGTTATGTCGAGGCTGTTCTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|109637318|gb|EC590863.1|EC590863
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 296

TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattg ... tacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaaatggccttttatttgtgtcaaattcttattgtttgtctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
                         aaattcttattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatattggtctgtcaaccagtttaaatggccttttatttgtgtcaaattcttattgtttgtctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC