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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatactattctagccttgattttttgagaaaaatataatgcatagatttttttacatatgtgcaagttctgttcttgtttaagaagtaggaatgct...

Basic information

species Zea mays
transcript GRMZM2G158789_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158789_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g62720.2 (Oryza sativa), 5'ss of exon 4
TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatactattctagc-cttgattttttgagaaaaatataatgcatagatttttttacat---atgtgcaagttctgttcttgtttaagaagtaggaatgct
||  | ||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |   ||||| | |        |||| |   || ||| ||  | |||   || |||     ||||| |  | ||| ||   | | |   
TCCGCAATGCTTCATAAAGCTCTGGAAGGCGCAGTGATGTTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtaagatactatccttgaatttgatctctgccttttcatatta-atattgatcttgctgcatttgatatgctcaggctgttttactgtaataatccgtatt---

upper sequence: GRMZM2G158789_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g02360.1 (Oryza sativa), 5'ss of exon 4
TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatactattctagc-cttgatt----ttttgagaaaaatataatgcatagatttttttacatatgtgcaagttctgttcttgtttaagaagtaggaatgct
||  | ||||| |||||||| |||||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||||| |||||||| || |   ||||||    | |||    |  |   |||| |    | |||||     || ||   |   | ||| ||| || |  || | |   
TCCGCAATGCTCCATAAAGCCCTGGAAGGCGCAGTGATGCTACACACTTTTCCAAAAACCACTGTTGATGTCTTTGCGTTGGTTCTTGAGTCTGGTGGCAgtaagatactatccttgaatttgattatgatattgctgcatttgatatgcttgtgctgttttagtgtagtacactgtagttacttattttagga--agaatt---

upper sequence: GRMZM2G158789_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G08170.1 (Glycine max), 5'ss of exon 4
TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatg-atac---tattctagccttgattttttgagaaaaatataatgcatagatttttttacatatgtgcaagttctgttcttgtttaag--aagtaggaatgct
   || ||||||||||||||| |||| || ||| |||| ||| | || || || ||||| ||||| ||||| ||||| ||||| || || ||| ||||||||| | ||||    | | |    |||||||| |    ||  | | ||| |||   ||||| |   || || || |      |    ||  |   | ||  ||    
AGTTCAATGCTTCATAAAGCTTTGGAGGGAGCAATAATACTGGAAACATTCCCCAAGACAACTGTGGATGTCTTTGCATTGGTGCTGGAATCTAGTGGCAgtaagcatacatacaatttcatattgattttctatttaatttgtcatg-atattgtttttgatggat-tgaaattaacagacaaaattgtgctgaatataaa----

upper sequence: GRMZM2G158789_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G27490.1 (Arabidopsis thaliana), 5'ss of exon 5
TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgta-----------tgatactattctagccttgattttttgagaaaaatataatg---catagatttttttacatatgtgcaagttctgttcttgtt-taagaagtaggaatgct------------------------------------------
||||| |||||||| |||||  ||||||| | | ||||| || | || |||||||| || || |||||||||||||| ||||||||||| ||||| || ||||           | |  | | |     |   ||| ||| |  | ||| | ||     || | ||   ||  | ||  |     |   || | |    ||    | ||| || |                                          
TCATCAATGCTTCACAAAGCATTGGAAGGTGTAATAATGATGGAGACGTTTCCAAAAACAACCGTTGATGTTTTTGCATTGGTTCTTGAATCTGGAGGAAgtaagtcttaacaataactcgactgctatcaaaattattttaccagaatgtgattgcttattggttcgcttggacattcgtggagttgattatggaagcaacttattggattgttgtttggcattttctgattttctccaatggtattgtattgcag

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|31612339|gb|CD568961.1|CD568961
EST:     TCCAAAGACCCCTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|87152491|gb|DY397280.1|DY397280
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|22491412|gb|BU051335.1|BU051335
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|31352976|gb|CD437333.1|CD437333
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|211446359|gb|FL080076.1|FL080076
EST:     CCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|19436120|gb|BM952530.1|BM952530
EST:     TCCAAAGACCACTGGTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|5901059|gb|AW042159.1|AW042159
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|78124719|gb|DV543103.1|DV543103
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|60344517|gb|DN211490.1|DN211490
EST:     CCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: CCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|60356164|gb|DN223137.1|DN223137
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|148997935|gb|EE035925.2|EE035925
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|60398212|gb|DN231028.1|DN231028
EST:     TGTTGATGTTTTTGCCTTGG-TCTGGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|14203944|gb|BG837621.1|BG837621
EST:     CCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTRTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|31351844|gb|CD436201.1|CD436201
EST:     TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
EST: gi|19351025|gb|BM895557.1|BM895557
EST:     TCCAAAGACCCCTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCA                         GTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG
genomic: TCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTG

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: 95

TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTGGAATCATGATGTATGACCTTGTTACATCTGTATCCGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 26

TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTGGAATCATGATGTATGACCTTGTTACATCTGTATCCGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTGGAATCATGATGTATGACCTTGTTACATCTGTATCCGTG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 18

TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatact ... ttcgtttcagGTGATCTTCCCATCATTATATCATGCGCTAGTCTTGCATTGGCAGATGCTGGAATCATGATGTATGACCTTGTTACATCTGTATCCGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCGATGCTTCATAAAGCTCTGGAAGGCGCAGTAATGCTGCACACTTTTCCAAAGACCACTGTTGATGTTTTTGCCTTGGTTCTTGAGTCTGGTGGCAgtatgatactattctagccttgattttttgagaaaaatataatgcatagatttttttacatatgtgcaagttctgttcttgtttaagaagtaggaatgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaagta