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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA

Basic information

species Zea mays
transcript GRMZM2G056572_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
   ||| || ||||   || |||||    || | |   |||| ||||||  |  | ||||||    |  |||||||  ||||||||||||| ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||| ||||||||||| ||||| ||         
--gtgctaagcactacattatcttattttgtatatgaatggactatgatcgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG--------

upper sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 6
-----gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttct--aatgcccatgctttgt-tctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
     ||   |  ||   |  ||||| |||     ||| | | |      || || ||  | |  ||     |  |  | | | || |||||| ||| | |||||||| || ||||||||||| ||||| |||||||| | |||| | ||||| ||||| ||||  ||||| || ||||          
gtaaggtcatcttatagttagtttttgttatttgatttatagattcttgttgtttgtctctatggaaattttaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG--------

upper sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 5
----------------------gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttctaatgcccat-----gctttgt-tctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
                        ||   | |||  |||  || |||   | ||  ||     |||||   |||  | || ||  | ||      | | |  | || |||||| ||| | ||||| ||||| ||||||||||| ||||| |||||||| | |||| | ||||| ||||| ||||  ||||| || || |          
gtaatgtcatcactcatcattaacatat-agtcagctttagtt-ttatttacttaattcaaaaaatatatatataatgcttatcactattgataacatcgcatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG--------

upper sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 5
--------gtatgccaatcacttttttttc--ttaaaaagtttcttggtggaatatgattatccttct--aatgcccatgctttgt-tctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
         | | | | | |  ||||| |   || |    ||    | |  |   || || ||  | |  ||   | |  |  | | | || |||||| ||| | |||||||| || ||||||||||| ||||| |||||||| | |||| | ||||| ||||| ||||  ||||| || ||||          
gtaaggttatcttctagttagctttttgttatttgatttattataagattcatcttgtttgtcactatggaaaatctaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG--------

upper sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
-----------------gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgat-tatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
                  |||    | |  |  ||||  |||   | ||   |      |||| || | |   |||  ||   |   |   |  || |||||| ||| | ||||| ||||| ||||||||||| ||||| |||||||| | |||| | ||||| ||||| ||||  ||||| || || |          
gtaatgtcatcattaacatatagtcagctttagttttatttatttaattc--taaaaagatataatgtttatctctgttgataacattacata-tacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG--------

upper sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 6
---------------------gtatgccaatcacttttttttcttaaaaagtttcttgg----tggaatatgattat-ccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
                      | | ||||  | ||  |  |   | ||||||||  |     ||| |  || ||    |||||||||       || ||| || |||||| ||| | ||||| ||||| ||||||||||| ||||| |||||||| | |||||| ||||| ||||| ||||  ||||| || ||||          
gtaaggacatcaatcgttaggtttttccaagta-ttaatcatagaacaaagtttccagtgatttggtaattgcttgcatcttctaatgattgaaattcgtt-tacagGAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG--------

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|26558429|gb|CA830664.1|CA830664
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|76917080|gb|DV166669.1|DV166669
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|5846990|gb|AW000069.1|AW000069
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|76288715|gb|DV028283.1|DV028283
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|60351289|gb|DN218262.1|DN218262
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|101386844|gb|EB815439.1|EB815439
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|149106821|gb|EE188718.2|EE188718
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|71448387|gb|DR829437.1|DR829437
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|166414080|gb|EG170970.1|EG170970
EST:     TGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|18660188|gb|BM500731.1|BM500731
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|5296366|gb|AI783136.1|AI783136
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|91051774|gb|EB162192.1|EB162192
EST:     TGATGAGCGGCAGCGTATTGAAAATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGT
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGT
EST: gi|149111016|gb|EE294515.2|EE294515
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|74237808|gb|DT645722.1|DT645722
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|60394530|gb|DN227400.1|DN227400
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|22133680|gb|BQ833845.1|BQ833845
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|61118718|gb|DN559679.1|DN559679
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|50323711|gb|CO518837.1|CO518837
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACA
EST: gi|76931265|gb|DV172687.1|DV172687
EST:     TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG                         GAACATGGCGCG
genomic: TGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAGgtatgccaat ... tgttctatagGAACATGGCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttcttggtggaatatgattatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA
                            ttctaat  putative branch site (score: 2)
                                          ctttgttct  putative PPT
               aatatgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC