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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttccctgaaattgaaccttgtatcttcttactatttggttattagaatattagtgctgaacctatgtcttatgcttcacag

Basic information

species Zea mays
transcript GRMZM2G074687_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g14270.1 (Oryza sativa), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttccctgaaattgaac--cttgtatcttcttactatttggttattagaatattagtgctgaacc-tatgtcttatgcttcacag
||||||||||||||||||||||| || |||||||||||||| ||||| ||||||||||||||  || |||  ||||||||  ||||    | |  | | ||  | | ||  | | |   | ||||||  | |   || || |||||||
AAAATCAAGAACCCTAACTACCAAGGCAAATGGAAGGCACCGATGATCGACAACCCAGgtataattgcctttaattgaacaacttggtattacacatttttcagatgttgaactctgcattctgaactgtttcctttgtggttcacag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtt---------tccctgaaattgaaccttgtatcttcttactatttggttattagaatattagtgctgaacctatgtcttatgcttcacag
|||||||||||||| |||||  | || ||||||||||||||  ||||||| |||||||||   ||         ||     | | | |   | ||| |   | || ||    ||| |||  | || |  | | | | ||    |   ||  |||
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacgcccttctacacagtagtaatatttatgtaaattcttttgcactataagataaata-tattcagcatttgaaaaacatttatcag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G28890.2 (Glycine max), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgt-------atgtttccctgaaattgaaccttgtatcttcttactatttggttat-tagaatattagtgctgaacctatgtcttatgcttcacag
|||||||||||||| |||||  | || ||||||||||||||  ||||||| |||||||||       |   |   ||  |    |    | | | |    | ||||| |   | ||  |||    |  | ||| | ||    |   ||  |||
AAAATCAAGAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattatacactcttctacaccgtagtaatatttttataaattattttgcattataagataaatatattcaacatttgaaaaacatttgtcag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgta--tgtttccctgaaattgaaccttgtatcttcttactatttggttattag--aatattagtgctgaacc----tatgtcttatgcttcacag-------------------------
 |||| || ||||| |||||| |||| |||||||||||||||||||||||||||||||||   ||  |     |  |  |   ||  || |  || |  | | | | ||    ||| ||| |    ||      ||| | ||   | ||  |                          
CAAATAAAAAACCCCAACTACAAGGGAAAATGGAAGGCACCTATGATTGACAACCCAGgttcttgcatattccacttcaacattttaatttgtttgcagtcttggtgttctttaatgttattttctaatactgatatattttcaacatcttaaatttgtgtgttttttgcctttttag

upper sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 8
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttccctgaaattgaaccttgtatcttcttactatttggttattagaatattagtgctga---acctatgt----cttatgcttcacag
||||| ||||| || |||||| |||| |||||||||||||| ||||||||||||||||||   | ||| || |  ||   ||| |||    |   |||||  |  || |  | | |    | |   || |||       | ||  || ||||
AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGACAACCCAGgttcctatccatgcacctgcttcttctatgccatagttattttttggtttgg-tctcaacattcagacacttataaactgttcatattttacag

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|110539727|gb|EE043647.1|EE043647
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|40337074|gb|CK371144.1|CK371144
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|148959987|gb|EE153226.2|EE153226
EST:     CAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: CAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|110963677|gb|EE183577.1|EE183577
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|211279487|gb|FL438453.1|FL438453
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|32846103|gb|CD985784.1|CD985784
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGT
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGT
EST: gi|7135086|gb|AW497909.1|AW497909
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|166545653|gb|EG129994.1|EG129994
EST:     CTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: CTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|31558808|gb|CD528020.1|CD528020
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|67010625|gb|CO439374.1|CO439374
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|211100464|gb|FL191945.1|FL191945
EST:     CAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: CAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|149112806|gb|EE295616.2|EE295616
EST:     GAACCCTAACTACCGGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|32945066|gb|CF049885.1|CF049885
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGT
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGT
EST: gi|7135470|gb|AW498102.1|AW498102
EST:     AACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: AACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|37397542|gb|CF636072.1|CF636072
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|148996194|gb|EE035466.2|EE035466
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|211100467|gb|FL191948.1|FL191948
EST:     ATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: ATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|67022234|gb|CO450983.1|CO450983
EST:     GAACCCTAACGACCACGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|4837470|gb|AI670560.1|AI670560
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|78022156|gb|DV490543.1|DV490543
EST:     GAACCCTAATTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAGGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
EST: gi|60672264|gb|DN475030.1|DN475030
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAAATACATT
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAA-TACATT
EST: gi|109637413|gb|EC590958.1|EC590958
EST:     GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAG                         ATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG
genomic: GAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTG

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), 48 (downstream exon)
Score: 367

AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTGGCATTGAGCTGTGGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 397

AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTGGCATTGAGCTGTGGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 343

AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTGGCATTGAGCTGTGGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 1774

AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttcc ... tgcttcacagATTTCAAGGATGATCCGTACATTTATGCATTTGACAGCCTGAAATACATTGGCATTGAGCTGTGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATCAAGAACCCTAACTACCAGGGTAAATGGAAGGCACCTATGATTGACAACCCAGgtatgtttccctgaaattgaaccttgtatcttcttactatttggttattagaatattagtgctgaacctatgtcttatgcttcacag

- - - - - - - - - - - - - - - TGGAAG