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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

Basic information

species Zea mays
transcript GRMZM2G076826_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 6
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcct--cacttgatcttacttgcatt-ctcacttgattttactt----gcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                        | |  |   ||| ||  ||||| |||   | |   |  ||      |||   || ||       |||| |     ||||    |  | |    || |||||   |||  | || | | ||     |||   || |  ||  ||||||||||||||||  |||| || || |||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||||  |  
-------------------gtctgaaaatcccttgaatc--attttcctttgaaaacacaaggactttggtcgaatagtatactactgcatggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttcatcactttgttggatttg--cagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCCTCTACATGACCTACAGTGGCGAGAACACCTTTGGGCTGCTCTAGGCGCG

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 5
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgctt---ccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                                                      | ||||   ||  | |   || |  |||     |||     |       |   ||     ||  |   || | | ||   || | ||  ||      ||        |||||||  |||||||| | |||||||| || ||||| ||||||||||| ||||| || ||||| |||||||| || ||||| || ||     ||||   |  
-----------------------------------------------------gtgagaaagaattcctt---tttaatattcaaatacacatatcgatgatgtagttt--ctgtaactat-ttattatttatattcatttatttgtattttgtgttatcacagCTGCCATGATGTCTGCCATCTATGAGGAAAACAAAGATGAGGATGGTTTCCTGTATATGACTTACAGTGGGGAAAACACATTTGGATCATTCTAACGGAA

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttg-agcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC-
                                                     |  ||       | |   || ||  |||      | | || | | || ||      |   || ||   | | ||  |  |    | |||||  |||  |  |    |||| || || ||||| || |||||||| ||  ||||||||||||| || || || ||||| |||||||| || |||||||| |||||   ||        || 
----------------------------------------------------cagcagggccagagccgggcgctgtggcacc----gccgtg-tgcaccgtcgctgtctttgctcacc-acgtccttgc--gcccctccttgcaaccc--actcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG-TGCCGGGGAGCAGCT

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------gtctg-gaaaataaatacagagacaacatacttctgactctgattttgc----------ttcctataagaa--ttgatggcattcgttgagcatt-tggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctg--tgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                |  | | || | |||  ||          ||| ||  |  |||||||           ||   ||   ||  |||  | | |  |    ||| |  |  ||  || |      |   ||||    |  |  ||     | | |  | |  |     |     | |  ||  |||||| ||| ||||||| || |||||||| ||| ||||||| || || || ||||| ||  | |||||||| ||||||||||| ||||||||      |||   
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtg-gcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactg---cagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S249_49V6.1 (Physcomitrella patens), 3'ss of exon 4
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGG-GCTCCTCTAGATGGC
                                       ||||| |  |   | ||  | |  |  ||  | ||   | |||||  ||   | | |   ||  ||| |  || |  |         || |  | |||  |||              |||||||||| ||||||| || || || || ||  ||||||||||||| |||||||| ||| | || ||||||||||| ||||||||||| | |  | |  |  | 
--------------------------------------ttgattctagtctgtgtattattgcactgctgttgtgtgggatttgttgatgggttacttaat--tcattgaatgtcgcac-------cattcaactttgtttg--------------tgcagCTGCTATGATGTCATCCATTTACGATGAACACAAGGATGAGGACGGATTCCTGTACTTTACTTACAGTGGTGAAAACACCTTCGGAGATGTTATCAACTG-

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 4
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC--
                                                                                         ||||    || ||   || | |||  || |  ||       ||||||    || | |  |   | | || ||| ||  |||| ||  | ||||| || ||| ||||||| |||||||||||||||||| | || ||||| || ||||| ||||||||   |    |||   |  
---------------------------------------------------------------------------------------gtatgag---ccgtcgagacgtaatcccacgtatat-------tgatttacactgttcctttc--cttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG--CCAAGAAGAACACTA

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 4
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC--
                                                                                         ||||    || ||   || | |||  || |  ||       ||||||    |  | |  |   | | || ||| ||  |||| ||  | ||||| || ||| ||||||| |||||||||||||||||| | || ||||| || ||||| ||||||||   |    |||   |  
---------------------------------------------------------------------------------------gtatgag---ccgtcgagacgtaatcccacgtatat-------tgatttacactattcctttc--cttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG--CCAAGAAGAACACTA

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|211035126|gb|FL190210.1|FL190210
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|211509914|gb|FL437411.1|FL437411
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|17931727|gb|BM268687.1|BM268687
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|18165025|gb|BM334870.1|BM334870
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|71441162|gb|DR822212.1|DR822212
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCCCCAACAG                         CTGCTTTGATGTTTTCAATTTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|91052588|gb|EB163006.1|EB163006
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCCCCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|18174937|gb|BM350325.1|BM350325
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|211192317|gb|FL065114.1|FL065114
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGACGAGGATGGGTTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|18169711|gb|BM339551.1|BM339551
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|71434664|gb|DR815714.1|DR815714
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|211194714|gb|FL065125.1|FL065125
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGA-CAAGGACGAGGATGGGTTCM
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|211192306|gb|FL065103.1|FL065103
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGSTCTGATGTCTTCAATCTATGAAGARAACAAGGACGAGGATGGGTTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|16918829|gb|BM073915.1|BM073915
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|16926343|gb|BM079411.1|BM079411
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|91052589|gb|EB163007.1|EB163007
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|6194643|gb|AW146747.1|AW146747
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAAGATGGGTTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|93016973|gb|EB642493.1|EB642493
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCCCCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|211194707|gb|FL065118.1|FL065118
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGACGAGGATGGGTTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
EST: gi|17930090|gb|BM267050.1|BM267050
EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                       ttgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC