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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttctgcttccctctaaagccatttatttgtgagtcttctgtacctttatttcattgtcgcccttcaaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTTTGCATCAAG

Basic information

species Zea mays
transcript GRMZM2G160430_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 12
gtaactttctgcttccctctaaagccatttatttgtgagtcttctgtacctttatttcattgtcgcccttcaaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTTTGCATCAAG
|||| || || ||||||  | ||  ||  | ||||| |||  |||||| |  ||    | || | | ||| |||||||||||| ||| || |||||||||| ||||||||||| |||||  ||||||||||||   |  ||
gtaatttcct-cttcccaatgaaatcacctttttgttagttgtctgtaacaataacatagtgactcactt-aaaattgcagATCTCTACTGCTGGGATGACTCTAAGCCTTCTTGCAGTATCTGTTGTATTTTTTCTGGAG

upper sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 12
gtaactttctgcttccct---ctaaagccatttatttgtgagtcttctgtacctttatttcattgtcgcccttcaaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTTTGCATCAAG
|||| | ||| | |||     |||||||    || || |  || ||||||  |  || |  |   || | ||||||  ||  |||| |||||| |||||||||| |||||||| || ||||||||||||||||||| | |||||
gtaattctcttcctcctgaaactaaagcatgctaattttctgtattctgtgaccataataaagc-tctcgcttcaac-ttctagATCTCTTCTGCTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG
















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|5296357|gb|AI783127.1|AI783127
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGTTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
EST: gi|32832825|gb|CD972503.1|CD972503
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
EST: gi|101387701|gb|EB815865.1|EB815865
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
EST: gi|37385615|gb|CF629958.1|CF629958
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
EST: gi|32927095|gb|CF031907.1|CF031907
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
EST: gi|148950293|gb|EC895852.2|EC895852
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT
EST: gi|5846979|gb|AW000058.1|AW000058
EST:     GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT                         ATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGTTGTTGTATTT
genomic: GTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATTgtaactttct ... aaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatttgtgagtcttctgtacctttatttcattgtcgcccttcaaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTTTGCATCAAG
                                       cccttca  CT-rich tract
                        tttatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactttctgcttccctctaaagccatttatttgtgagtcttctgtacctttatttcattgtcgcccttcaaaattgcagATTTCTTCTTCTGGGATGACCCTAAGCCTTCTGGCAGTTGCTGTTGTATTTTGCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT