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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtccctccacccgtatccgtatccgcctccccaatccccatctagggttcacttcactccgactcaatcctccgctggcgtctcgctcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG

Basic information

species Zea mays
transcript GRMZM2G075584_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075584_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g50050.2 (Oryza sativa), 3'ss of exon 1
gtccg--tccctccacccgtatccgtatccgcctccccaatccccatctagggttcacttcactccgactcaatcctccgctggcgtctcgctcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG
|| ||  |   |||||||  |  |    ||    |  | || |   |||||||||| | || |||  ||  |         ||   |||| |||  |   |||| |||||||| ||||| |||||||||||||||  |||||||||||| |||||||||||||||||||||||| | |||||||| ||||||||||||||||
gttcgattgtttccacccccaatc---cccaatccatcgattcgattctagggttctcctctctc--accta---------tgcaatctcactctaccctagGATGTGATTGCTTGCGATGTCATCAACCCCGACCACATCGACGTCGAGTTCGATTCCATCGGCGGCCTCGACCACGTCAAGCAGGCGCTCTACGAGCTCG
















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|211205458|gb|FL094087.1|FL094087
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211208035|gb|FL094099.1|FL094099
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211208028|gb|FL094092.1|FL094092
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211205453|gb|FL094082.1|FL094082
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTG
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTG
EST: gi|211208033|gb|FL094097.1|FL094097
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GWYGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|148935813|gb|EC879860.2|EC879860
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|148964391|gb|EC905767.2|EC905767
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|37426408|gb|CF650956.1|CF650956
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGT
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGT
EST: gi|211208032|gb|FL094096.1|FL094096
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211205457|gb|FL094086.1|FL094086
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211208030|gb|FL094094.1|FL094094
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGT-CGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|93014430|gb|EB639950.1|EB639950
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|71315784|gb|DR794534.1|DR794534
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211208029|gb|FL094093.1|FL094093
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         NNN-TGATTGCGTGCKACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211208034|gb|FL094098.1|FL094098
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211208031|gb|FL094095.1|FL094095
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCACCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|74245966|gb|DT653880.1|DT653880
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211205459|gb|FL094088.1|FL094088
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211205454|gb|FL094083.1|FL094083
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GWNGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
EST: gi|211205456|gb|FL094085.1|FL094085
EST:     AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAG                         GACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC
genomic: AGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTC

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), 45 (downstream exon)
Score: 59

CCTCGATCCCAACCGCGCCGCCTCTCAGAAGGCGCAGCAGCAGAAGAAGGAGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 89

CCTCGATCCCAACCGCGCCGCCTCTCAGAAGGCGCAGCAGCAGAAGAAGGAGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

CCTCGATCCCAACCGCGCCGCCTCTCAGAAGGCGCAGCAGCAGAAGAAGGAGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 194

CCTCGATCCCAACCGCGCCGCCTCTCAGAAGGCGCAGCAGCAGAAGAAGGAGATCGCCAAGCGCCTCGGCCGGCCCCTCGTCTCCACCACGCCCTATGAGgtccgtccct ... tcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagggttcacttcactccgactcaatcctccgctggcgtctcgctcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG
                                          cgctcac  putative branch site (score: 194)
                                       tctcgctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtccctccacccgtatccgtatccgcctccccaatccccatctagggttcacttcactccgactcaatcctccgctggcgtctcgctcaccgacagGACGTGATTGCGTGCGACGTCATCAACCCCGACAGCATCGACGTCGAATTCGATTCCATCGGCGGCCTCGACAAGGTCAAGCAAGCGCTCTACGAGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG