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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagttatgatgttttgaatatttaatgcag

Basic information

species Zea mays
transcript GRMZM2G107362_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 6
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagtt----atgatgttttgaatatttaatgcag
 ||||||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| ||||| || |||||||||||||||||||||||||| |||||   |  ||||  |   | | |||  |   |    ||||  |||  ||  |  ||||     |||    || ||| ||  ||||||
GATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTCCAGCGAACCATGCTTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgc--cactgctttgcatatgttatatgt-gccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 6
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagt-tatgatgttttgaatattta-atgcag----------------------------------------------------------
 ||||| ||||||| |||||||||||| ||||| || |||||||||||||| |||||||| |||||| | ||||| |||||||| ||||| || || |||||| |    |  | | ||    |    |      | || || ||||  ||      | |    |||| | || |   | ||| |                                                           
GATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGTACTATGCTGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaaagg--agctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 6
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagttatgatgttttgaata----tttaatgcag----------------------------------------------------------------------------------------------
 ||||| ||||||| |||||| ||||| ||||| || |||||||||||||| |||||||| || ||| | ||||| |||||||| |||||||| || |||||| |    |  | | ||  | ||||    |   |  ||||  ||     |   |  |    |||| |||| |    | |    |||                                                                                              
GATGGAATCTGGAAGTGGCAATGGTGATAGTGAGGTACAGCGTACTATGCTGGAACTTCTCAATCAGTTGGATGGATTTGAAGCTTCAAACAAGATCAAGgtaaagg--agctatactgttatgtgtattaaggggaattttaaagctagtcttatgtccactgttctgaaaagaaatctgtaacagttgaacttaacagatattatttactctgtctgactcatttgagatgagttctcaattctttgtggaggttctgaagataaattttcaattgtag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 6
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcac-ttgtgctc---------ctgtgtgctggat-----------------tagtgatttgtaaatgtata-acagttatgatgttttgaatatttaatgcag
 ||||| ||||||| ||| || ||||||||||| || || || || ||||| || ||||| || || || || ||||||||||| ||||||||||| |||||||  || |  ||||             |  |  | || ||                 | ||  | || || ||   | | ||| ||  | | || |||   |  |||||
TATGGAATCTGGAAGTGGAAATGGTGACAGTGAGGTGCAACGGACCATGCTCGAGCTTCTCAATCAACTTGACGGTTTTGAAGCGTCAAACAAAATCAAGgtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtga---tttgtaaatgta--taacagttatgatgttttgaatatttaatgcag
|||||| ||||||||||| || ||||| |||||||| ||||| |||||| | || ||||| || || || ||||| |||||||| |||||||| || ||||||| | ||| |  |    ||  ||      | ||| |   |||||   ||||  ||||  || | |||   |||  ||||| | |||
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgt-atgagatgaccatttattacag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 6
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtaca--catcacttgtgctcctgtgtgct---ggattagtgatttgt----aaatgtataacagttatgatgttttgaatatttaatgcag------------------------------------------------------------------------------------------
 ||||| || |||| |||||| ||||| |||||||| ||||| |||||||| || ||||| || || || ||||| ||||||||||| ||||| || || ||||    |  | |||    ||| | ||||   |   ||||  | |||    |  ||||| | | || ||   || |   ||||   ||                                                                                             
TATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGGACTATGCTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCATCCAACAAGATAAAAgtactattaataattgctaccctttttgcttctgctgtagttgtgtgtgcccacttgtattatatttgtgtatttatatgtattatgtgtgtggtatttgttatctagtagaatcagcaaaatggttggaaattggtggaatctgtatgtcatatctgtgacaacatgatcaatattttcag

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|60354034|gb|DN221007.1|DN221007
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|67018679|gb|CO447428.1|CO447428
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|32843443|gb|CD983124.1|CD983124
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|6564061|gb|AW231683.1|AW231683
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|110525764|gb|EE029948.1|EE029948
EST:     AAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTTTGAGG
genomic: AAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|86470516|gb|DY236886.1|DY236886
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|32929081|gb|CF033893.1|CF033893
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|60398374|gb|DN231190.1|DN231190
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|60354159|gb|DN221132.1|DN221132
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|33095260|gb|CF055254.1|CF055254
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTTGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|67016311|gb|CO445060.1|CO445060
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|211487780|gb|FL049401.1|FL049401
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAG-CCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|32846355|gb|CD986036.1|CD986036
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACACAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|60350083|gb|DN217056.1|DN217056
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|211122652|gb|FL433068.1|FL433068
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|5847445|gb|AW000524.1|AW000524
EST:     TTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|60355211|gb|DN222184.1|DN222184
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
EST: gi|20301129|gb|BQ164072.1|BQ164072
EST:     TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAG                         GTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG
genomic: TTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGG

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: 434

AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 489

AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatca ... tttaatgcagGTTTTGATGGCAACGAACAGAATAGACATTTTGGATCAAGCCCTTCTGAGGCCTGGCCGCATAGACAGGAAGATTGAATTTCCAAATCCTAACGAGGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtgatttgtaaatgtataacagttatgatgttttgaatatttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC