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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcccgtagctcaaaacaaaccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA

Basic information

species Zea mays
transcript GRMZM2G178415_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
------------gcaagcccgtagctca-aaacaaaccgactgcttt---ctgcaatgttt-tctgatcccctctgtatcccg-ttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA
            |  ||    | ||  | ||| |  || || ||       || |   ||| |||||    || | | ||    |||| ||  ||||||||||| ||||||||||| ||||| || || ||||| || || ||||| ||||| |||||||||||||||||||||||||| || 
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG

upper sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 8
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 7
gcaagcccgtagctcaaaacaaaccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA
           |   |  | ||| | |           || |||||||         || ||    ||   |  ||||||  |  ||||||| ||| || |  | || |||||||| || || ||||| || || |||||||||||||||||||| |||||||| 
-----------gtataggaaaaatcaa-----------aaagttttctagattgaattg-atggt-ttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

upper sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 8
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 7
gcaagcccgtagctcaaaacaaaccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA
           |    | | |||   |  |||||||| | ||       |||       |||    ||   |  | ||||  |  | ||||||||| || |  |  | || |||||  |||| ||||| || || |||||||||||||||||||| |||||||| 
-----------gtatgagaaaaataaaaagctttctggattg------aatc-------tatggttttttgtgactagATTTTTGCGAAGAAAGGCATCATTGTGTTGCCAGACATCTTGGCAAACTCAGGAGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

upper sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 8
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 7
gcaagcccgtagctcaaaacaaaccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA
           |   |  | ||| | |           || |||||||         || ||    ||   |  ||||||  |  ||||||| ||| || |  |||| |||||||| || || ||||| || || |||||||||||||||||||| |||||||| 
-----------gtataggaaaaatcaa-----------aaagttttctagattgaattg-atggt-ttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

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|6851580|gb|AW352590.1|AW352590
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|60344011|gb|DN210984.1|DN210984
EST:     AGTACATCATCAAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|71766898|gb|DR964835.1|DR964835
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|67040711|gb|CO466966.1|CO466966
EST:     ACTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|6012198|gb|AW061740.1|AW061740
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|148934217|gb|EC878238.2|EC878238
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|148981457|gb|EE027656.2|EE027656
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|101387651|gb|EB815840.1|EB815840
EST:     ATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGGGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: ATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|148974520|gb|EE025306.2|EE025306
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|6993922|gb|AW453136.1|AW453136
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGG
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGG
EST: gi|91053893|gb|EB164311.1|EB164311
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|78092009|gb|DV520383.1|DV520383
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|60394477|gb|DN227347.1|DN227347
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|211079581|gb|FL056327.1|FL056327
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|60343914|gb|DN210887.1|DN210887
EST:     CATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: CATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|71426411|gb|DR807461.1|DR807461
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|211375022|gb|FL430803.1|FL430803
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|50330055|gb|CO525181.1|CO525181
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|86470639|gb|DY237009.1|DY237009
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|148940230|gb|EC884999.2|EC884999
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|14243831|gb|BG841522.2|BG841522
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|74245082|gb|DT652996.1|DT652996
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|148934216|gb|EC878237.2|EC878237
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|78077525|gb|DV505959.1|DV505959
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGAGGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|60357158|gb|DN224131.1|DN224131
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|71328973|gb|DR801176.1|DR801176
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|211079579|gb|FL056325.1|FL056325
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCT
EST: gi|5847156|gb|AW000235.1|AW000235
EST:     AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAG                         ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCC
genomic: AGTACATCATCGAGGCTGCCAATCACCCCACAGATCCAGAGGCAGACGAGgcaagcccgt ... ccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA
                     ttctgat  putative branch site (score: 3)
                                      tcccgttccatcccc  putative PPT
               aatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagcccgtagctcaaaacaaaccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG