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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG

Basic information

species Zea mays
transcript GRMZM2G020446_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 6
gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
   |    || | |   | | || | ||||||       |||| |  ||  | | |  |||| |||  |||||||||||||||  |||| |||||||| ||||| ||||||||||||||||||||||| ||||||||| |||||||| | ||||| ||||| |||
-gtttgaccatatcttgtgttttctttttgatat-----ccttgttggtaccctacaaacatattgcgcttgtagGGAGCTGGTTTGGTGGTTCATGACGCAGGAGCCTACTGCATGAGCATGGCTTCAACCTACAACTTGAAGTTGCGACCACCTGAATATTGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G36580.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
                                                                   | |||| | || | |         |||   |    ||  |  | |||       || ||    |   ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || || || |||
gtaatatcatatatttatcttttgttatatagttgcttacataataataatatacatgcataatctatgcaaaactatgacaaagacaacaatgccaacttgtttaaactatctcatctgaattttaatgtc--agGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTAAAGATGCGGCCTCCTGAGTATTGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G33830.2 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctt-tctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG----------
                                                                     | |||| |||  | |         |||   |    ||  |  | |||  |||||    || |  | | ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || || || |||          
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctga---attttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGGGTATGAAATC

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G33830.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctt-tctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
                                                                     | |||| |||  | |         |||   |    ||  |  | |||  |||||    || |  | | ||||  ||||  |||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||| || |||| || || || |||
gtaatatataatatatttatcttttgttatatagttgcttaaataataataatatacacgcataatgtatgcaaaaccacgacaaagacaacaatgccaacttgtttaaactgtctcatctga---attttaatggcagGGTACTGGTTTGGTTGTTCATGATGCTGGTGCTTATTGCATGAGCATGGCATCAACCTACAATCTTAAGATGCGGCCTCCTGAGTATTGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G11880.1 (Arabidopsis thaliana), 3'ss of exon 6
gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgt---ccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
     | | | |   ||   ||| | ||||     |           |  |||   |    | ||||   | ||  |||||||||| ||||| |||||||| || ||||| ||||| ||||| ||||||||||| ||||| || ||| || | || ||||||||||||
----gtattataaggatctgattatgtttggcagctcaagtaatatggaatctaattagtttcttgtatacgttacagGGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G14390.1 (Arabidopsis thaliana), 3'ss of exon 6
gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgt---ccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
   | |   || |  || ||  | | || || | | |||   | |  |  ||||       | ||||   | ||  |||||||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||| || ||| || | || ||||||||||||
--gtatgataaggatatgattctgt-ttggaagctcaggtaatgtg-gaatcttatgagtttattgtattcattacagGGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGCATGGCTTCCACTTACAATCTCAAGATGCGTCCTCCGGAATACTGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv03s0038g04490.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------gtctctttcaaagccattatattttatttgatgattaggc---------cttctatgtttctttctgacatgttgtcct----tgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
                                     ||      | |    |||| | ||  || ||  ||||||         | || ||  || || ||||  |   || ||    |  ||||||||||  |||||||||||||||| ||||| ||||||||||||||||| || || ||||| || ||| || | ||||| || ||||||
gtaatgagcttggtcttttctaggggatgtatggacatcggccatataaattttatttatttatttatttttaggctgcaataatcgtcaatagtt-ttgctgatttagagttctacttttcagGGAGCTGGCTTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCAACTTACAATCTCAAGATGCGCCCACCTGAGTACTGG

upper sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0070g00580.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------gtctctttcaaagccattatattttatttgatgattaggc---------cttctatgtttctttctgacatgttgtcct----tgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
                                    |       | |    |||| | ||  || ||  ||||||         | || || ||| || ||||  |   || ||    |  |||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||  | ||||| || ||| || | ||||| || ||||||
gtatgagcttggtcttttctaggggatgtatggacattggccgtataaatcttatttatttatttatttttaggctgcaataatcgtcgatattt-ttgctgatttagagttctacttttcagGGAGCTGGCCTGGTTGTTCATGATGCGGGTGCTTACTGCATGAGCATGGCATCATCTTACAATCTCAAGATGCGCCCACCTGAGTACTGG

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|16379536|gb|BI993011.1|BI993011
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|76928256|gb|DV171541.1|DV171541
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCACCCCCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|211042194|gb|FL157904.1|FL157904
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTT
EST: gi|13515636|gb|BG517912.1|BG517912
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|78123739|gb|DV542123.1|DV542123
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|13515648|gb|BG517924.1|BG517924
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|211042195|gb|FL157905.1|FL157905
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|211076903|gb|FL402120.1|FL402120
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|148934358|gb|EC878387.2|EC878387
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
EST: gi|50329918|gb|CO525044.1|CO525044
EST:     AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAG                         GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT
genomic: AGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCT

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: 128

CACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

CACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 60

CACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

CACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATAGGGAACTTCCAACACCTGATGAGgtctctttca ... gtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatttgatgattaggccttctatgtttctttctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG
                                 ttctgac  putative branch site (score: 107)
                                           ttgtcctt  putative PPT
     atttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctttcaaagccattatattttatttgatgattaggccttctatgtttctttctgacatgttgtccttgtagGGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG