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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttccttctccttccttccttcctccctccatccacgcgcaacacggccgtgttagttataattcgcttcgcttctactgttccatgtccaatcgtc...

Basic information

species Zea mays
transcript GRMZM2G051842_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051842_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 5'ss of exon 1
GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttccttctccttccttccttcctccctccatccacg-cgcaacacggccgtgttagt-tataattcgcttcgcttctactgttccatgtccaatcgtc--
||||||||| |||||||| |||||||| |||||||||||||||||||||||||||||||||||| ||||| |||| |||||||||||||| || |||||||| | |||| ||||   || || | |  |   ||  ||     || | |       ||  | | ||| |  ||     |||| ||||   ||  |  ||     
GGTGCTGGGCCTGCAGCTGTCGGCGCTCATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCAACCGCATCCCCGGCGACCGCGGCGGTTCACAGCAGgtacctcctcctcc---ctaccatacaactaacacgcataattcacctcaatttctttgctctgtaactgtctgtaactcta-tgttaattgatccttctgaat
















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|211494759|gb|FL095205.1|FL095205
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211497636|gb|FL095208.1|FL095208
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|101385267|gb|EB814679.1|EB814679
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494757|gb|FL095203.1|FL095203
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494758|gb|FL095204.1|FL095204
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211491872|gb|FL095188.1|FL095188
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211497635|gb|FL095207.1|FL095207
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494747|gb|FL095193.1|FL095193
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494745|gb|FL095191.1|FL095191
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|37423776|gb|CF649617.1|CF649617
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494750|gb|FL095196.1|FL095196
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494752|gb|FL095198.1|FL095198
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGNTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211491870|gb|FL095186.1|FL095186
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494751|gb|FL095197.1|FL095197
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494753|gb|FL095199.1|FL095199
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|37425242|gb|CF650359.1|CF650359
EST:     ACTGGTCCCTCCTCGACCGCGTNCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|37423890|gb|CF649675.1|CF649675
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494755|gb|FL095201.1|FL095201
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494754|gb|FL095200.1|FL095200
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|28361854|gb|CB240210.1|CB240210
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494756|gb|FL095202.1|FL095202
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211497634|gb|FL095206.1|FL095206
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
EST: gi|211494748|gb|FL095194.1|FL095194
EST:     ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAG                         GTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC
genomic: ACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATC

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), 49 (downstream exon)
Score: 111

GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATCCTTCCTTCCCACAATGATCTCACCCCAATAACTACAATAGCCGGTGGAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 48

GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATCCTTCCTTCCCACAATGATCTCACCCCAATAACTACAATAGCCGGTGGAA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 72

GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATCCTTCCTTCCCACAATGATCTCACCCCAATAACTACAATAGCCGGTGGAA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 50

GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttcctt ... ctgtttacagGTGTCCATTGTGGAGTTGAATCATATTCTTAATGAAGTGAATACCCACATCCTTCCTTCCCACAATGATCTCACCCCAATAACTACAATAGCCGGTGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCTGGGGCTGCAGCTCTCGGCGCTGATCGACCACGTCGCGCGCGTCGACTGGTCCCTCCTCGACCGCGTCCCTGGCGACCGCGGCGGCTCGCAGCAGgtgcttccttctccttccttccttcctccctccatccacgcgcaacacggccgtgttagttataattcgcttcgcttctactgttccatgtccaatcgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctcc