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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag

Basic information

species Zea mays
transcript GRMZM2G107362_T04
intron # 4
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 4
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaacct-tttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag
|||||||| ||||| ||||||||||| || || |||||||| ||||||||||| ||||||||||||||   |  ||    || | |||||||| |  |   |  ||||  | |  |  ||||| |   |   | |||   ||||||
GTCATTGAACTTCCTATCAAACATCCAGAGCTATTTGAGAGTCTTGGAATTGCCCAACCAAAGgtttgaacttcttaac-aatatcatcttaaacgatcctatttttaagtattagcagaaaatattaactctcttt---tttcag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag---------------------
||||||||||| |||||||||||||| || |||||||| || ||||||||||| |||||||||||    |||||  |||   |    |  |||  |||   | |  |   | ||        |  |  | || ||   ||| | |                     
GTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgt--agtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag------------------
||||||||| | |||||||||||||| || |||||||| || ||||||||||| |||||||||||  || |    |||||  |    |  |||  |||   | |  |   | |         |  |  | || | | |  |  |                   
GTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAGgta-gtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag-
|||||||| || |||||||| ||||| ||| ||||||||   |||||||||||||| ||||||||    ||   |||   |||   ||||  |   |        ||  || |  | |||  ||  | |  |   | | ||| |  
GTCATTGAACTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttgaatttc-aaagcttatctatattgtgacgctgctaagtggatttcgaactgattgcttctccctctcttttaag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaaga--cggatcttgtttgtttttcag
||||||||||| |||||||| ||||| ||| ||||||||   |||||||||||||| ||||||||    ||   | ||  |    | |||  |  || |||   |   | || | |   |   |  |  ||||   |   |||  ||
GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAGgtacacttgaatcttaaaccttcttctccatattgtgatgatgctaagtggattagacgtaatctcatctctctgtctttctag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttttgaagaccatcttaaccttttgaactttacatgtaggtggaaaagacggatcttgtttgtttttcag---
||||||||||||||||| ||||| || |||||||||||||| |||||||| || |||||||||||  |||||  || | | |         | |   || |   | | | |    |  |  |    ||| ||| ||  |||  |    
GTCATTGAGCTTCCAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAGgta-gttttagttgtagtattttgctggagc---ttaagtatcataagc--ttttattaatttgattttgatttctttataacag

upper sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttcttttt------------tgaagaccatcttaaccttttgaac--tttaca---tgtaggtggaaaagacggatcttgtttgtttttcag-
|| ||||||||||||||||| ||||| ||| | ||||| || ||||| || || |||||||||||   |  | | |||            ||   | | | || |  | | |||    |||||   |||   || || || |  |||     || ||||    
GTTATTGAGCTTCCAATCAAGCATCCTGAATTATTTGAAAGTCTTGGTATAGCTCAACCAAAGgtacttcctttatttgtagttacatcatgtgtatcttattcatgtctcgaaggacttacaccttgtttttgaaatagcccaatcaaagatgcttttattg

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|32837096|gb|CD976774.1|CD976774
EST:     CAATCAAACATCTGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|32837479|gb|CD977157.1|CD977157
EST:     CAATCAAACATCTGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|32846543|gb|CD986224.1|CD986224
EST:     CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGACACAGGAAAGACATTGTTGGCACGT
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|20301129|gb|BQ164072.1|BQ164072
EST:     TTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: TTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|32928502|gb|CF033314.1|CF033314
EST:     CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|32848420|gb|CD988101.1|CD988101
EST:     CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|60398970|gb|DN231786.1|DN231786
EST:     CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTG
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTG
EST: gi|32836218|gb|CD975896.1|CD975896
EST:     CAATCAAACATCTGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGG
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGG
EST: gi|5847445|gb|AW000524.1|AW000524
EST:     CTTGGAATTGCACAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: CTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
EST: gi|32836397|gb|CD976075.1|CD976075
EST:     CAATCAAACATCTGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG                         GGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT
genomic: CAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGT

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), 48 (downstream exon)
Score: 238

GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 205

GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 167

GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

GTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGgtttgttttc ... tgtttttcagGGTGTCCTTCTTTATGGACCTCCGGGCACAGGAAAGACATTGTTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG