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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 12
gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG-----
|||||     | ||||| | |||||||  || |   |  | ||  ||     |  || |  | | | ||  | ||   |  |   ||   | ||  | || |||||||||||||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| || ||||||||||||     
gtatg----ttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatc-tgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAGGTTCT

upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 12
gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG
|||||     | ||||| | |||||||  || |   |  | ||  ||     |  || |  | | | ||  | ||   |  |   ||   | ||  | || |||||||||||||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| || ||||||||||||
gtatg----ttgctttgcttcactcatcttactaacaaagaatgatacctagtatttctgcacgatacatcttttttttggtctcatgtttgatc-tgttatttcagTGGTTGGTCCAAATGGTATTGGCAAATCCACTATACTTAAACTAATATCTGGAGATCTTCAGCCAACTTCAGGGACAGTGTTCCGCTCTCCCAAG

upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgttt-cagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG
 ||  || |   | ||  |           | | ||  |  | | ||||| |  |  | ||       | |  ||   | || ||     |        ||||| |||||||||| || ||||| ||||||||||| |||||||| ||  ||||| |||||||||| ||||| | |||||| || || || || ||| | |||
-tactatataaacctt--tttgtgggggagaatgttgtt--aaaataatgacatgactctg---ccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG

upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------------------------------------------gtatgatttcttctttgttc---cactcattgtagtcttactg--catattaatgtctggtttttgaagttg----cagttcttccatttttaaatcc---ctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG
                                                                 | || | |  | |||     ||   | || ||  | |  |  ||| |  |  |     |||||| |||     |||   ||  |  | || ||      |  | |||   || ||||||| || || ||||| ||||| || || || ||||| ||||| |||||||| |||||||| ||||  ||||||||||| || || ||| | |||
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG

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|211429010|gb|FL174619.1|FL174619
EST:     CCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|60343993|gb|DN210966.1|DN210966
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|32930219|gb|CF035031.1|CF035031
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|71307301|gb|DR789831.1|DR789831
EST:     AAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: AAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|12970170|gb|BG266849.1|BG266849
EST:     CCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|60352803|gb|DN219776.1|DN219776
EST:     AGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: AGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|211429008|gb|FL174617.1|FL174617
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|67015572|gb|CO444321.1|CO444321
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|78544243|gb|DV621741.1|DV621741
EST:     CTT-TTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|40336236|gb|CK370306.1|CK370306
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|211429006|gb|FL174615.1|FL174615
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|32932155|gb|CF036967.1|CF036967
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|32932545|gb|CF037357.1|CF037357
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|86472924|gb|DY239294.1|DY239294
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACACCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|211429005|gb|FL174614.1|FL174614
EST:     CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAT                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: CTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
EST: gi|20802514|gb|BQ293564.1|BQ293564
EST:     AGCCGCATAGCAA                         TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG
genomic: AGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTG

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: 301

TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAAgtatgatttc ... cttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG
                                  tccctcattgtctt  CT-rich tract
                     ttccatttttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatttcttctttgttccactcattgtagtcttactgcatattaatgtctggtttttgaagttgcagttcttccatttttaaatccctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG