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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgatcccctccgacccgtctccttcacccgccgggatttaatctcgcgtagcctcaccgtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG

Basic information

species Zea mays
transcript GRMZM2G128995_T06
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 1
gtaagcgatcccctccgacccgtctccttca------cccgccgggat--ttaatctcgcgtagcctcaccgtc-----cgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG
|||||| |||| | ||| |     ||||||       ||  |||  |     |  ||| |    |  | ||| |     | |||||||||||||||| ||||||||||||||||| |||||||| |||||||| ||||| ||||| |||||||||
gtaagc-atcctccccgccttccttccttccttccttccttccgccaccaccatcctcaccctcctcctccgcctcccgcccgcagTTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAG

upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 1
-----------------------gtaagcgatcccctccgacccgtctccttcacccgccgggatttaatctcgcgtagcctcaccgtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG
                        | |    |    |   |||     ||  | | | |    | ||   ||| | |   | | ||     ||||||||||| ||||  ||||||||||||| ||||| ||||| |||||| | ||||| |||||   |||||||
gtaagtactctctctctctacacatcactttttttttataaccaacgaccaccgcgc-ctcttacttttcctctcattttccctccaaattcgcagTTCAACATCCCCAATCTCCGCGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATACCGTCAAG
















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|211136925|gb|FL422189.1|FL422189
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211377201|gb|FL412470.1|FL412470
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211539519|gb|FL409049.1|FL409049
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211363177|gb|FL385284.1|FL385284
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211441636|gb|FL403705.1|FL403705
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211202638|gb|FL424402.1|FL424402
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTMTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211247493|gb|FL399189.1|FL399189
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211504705|gb|FL413781.1|FL413781
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|149102700|gb|EE288050.2|EE288050
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|15312764|gb|BI478361.1|BI478361
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211264685|gb|FL426671.1|FL426671
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAASGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
EST: gi|211217327|gb|FL397497.1|FL397497
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACCCCGCTCTACCGCgtaagcgatc ... gtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgtctccttcacccgccgggatttaatctcgcgtagcctcaccgtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG
                                     gcctcac  putative branch site (score: 3)
                      atttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgatcccctccgacccgtctccttcacccgccgggatttaatctcgcgtagcctcaccgtccgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTCCTCGCGCTCAGTGACGACCTCGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC