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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaacaatatttctgacagtgatacttattcgtttaggaacttatgtaatgatgaaacagaagctcactcttattaatctctttgttttaccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCGTACTTGTTACTCCTCTAGGAGCTCTAAGCATCATATTTAG

Basic information

species Zea mays
transcript GRMZM2G092991_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092991_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g29510.1 (Oryza sativa), 3'ss of exon 3
ataaaacaatatttctgacagtgatacttattcgtttaggaacttatgtaatgatgaaacagaagctca----ctcttattaatctctttgttttaccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCGTACTTGTTACTCCTCTAGGAGCTCTAAGCATCATATTTAG
   || ||| ||    || | |||||||||   ||  |  ||  | ||| || ||||| | ||||||||     | ||  |||||   ||||||||||||||||||||||| ||||||||||| || |||||||||||||||||||| || || |||||||||||||||||||||||||| ||||| ||||||||
---aatcaacatactggatactgatacttagatgtgaaccaatatttgtgat-atgaaccggaagctcaaacgttattcctaatcatcttgttttaccttgcagTGATTCTGGGCGAGGTAGCAAACTTTGCAGCATATGCATTTGCTCCCGCTGTACTTGTTACTCCTCTAGGAGCTCTTAGCATTATATTTAG

upper sequence: GRMZM2G092991_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G28580.1 (Glycine max), 3'ss of exon 3
ataaaacaatatttctgacagtgatacttattcgtttaggaacttatgtaatgatgaaacagaagctcactcttattaatctctttgt---tttac---cttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCGTACTTGTTACTCCTCTAGGAGCTCTAAGCATCATATTTAG
       | || |  |   | |   | | | |  |||   ||  |  |  |  ||   |   ||  |   ||   | | ||| | |||    ||||    ||| ||||||| | || || ||||||||||||||||| ||||||||||| |||||  ||||||| |||||| | |||||| |||| ||||| || ||
------tagtactcttataactataaataactaatttgctaatgtccgcgacaatcttatgaaaatttcatcaactaattctatatgtatgcttacatttttgtagTGATTGTTGGGGAAGTAGCCAATTTTGCAGCTTATGCATTTGCTCCTGCACTACTTGTAACTCCTTTGGGAGCTTTAAGTATCATTTTCAG

upper sequence: GRMZM2G092991_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT4G13800.1 (Arabidopsis thaliana), 3'ss of exon 2
ataaaacaatatttctgacagtgatacttattcgtttaggaacttatgtaatgatgaaacagaagctcactcttattaatctctttgtttta--ccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCGTACTTGTTACTCCTCTAGGAGCTCTAAGCATCATATTTAG
 |   |||   |||   |      |   |||| | ||   ||   ||| |      |    |    | |    || || | | ||  |  ||   |||  ||||||| | || ||| |||||||||||||||||||||||||||| || ||  | || || || ||| | |||||| |||| || || || ||
ttgggacatgttttggaatccaagtttctattggattt--aatcaatggacatcaaactttggttatgataactaatattgtattcatactaattcttatagTGATTGTTGGGGAGATAGCCAATTTTGCAGCATATGCATTTGCACCGGCTATTCTAGTAACACCTTTGGGAGCTTTAAGTATTATTTTCAG

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|76284893|gb|DV024461.1|DV024461
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
EST: gi|211462037|gb|FK972950.1|FK972950
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
EST: gi|211464551|gb|FK972952.1|FK972952
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAG
EST: gi|211464550|gb|FK972951.1|FK972951
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
EST: gi|211462034|gb|FK972947.1|FK972947
EST:     AGGCTTCTCATATCTATATGAGCCGTTAWGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
EST: gi|211462036|gb|FK972949.1|FK972949
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGSCG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
EST: gi|76920481|gb|DV168194.1|DV168194
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTTGCAGCATATGCATTTGCCC
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTT-GCAGCATATGCATTTGCCC
EST: gi|211462031|gb|FK972944.1|FK972944
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG
EST: gi|211462030|gb|FK972943.1|FK972943
EST:     AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTA                         TGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGC-G
genomic: AGGCTTCTCATATCTATATGAGCCGTTATGGTGGTTGGGAATGATAACTAgtaagtgtca ... taccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaatgatgaaacagaagctcactcttattaatctctttgttttaccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCGTACTTGTTACTCCTCTAGGAGCTCTAAGCATCATATTTAG
                            tattaat  putative branch site (score: 2)
                                  tctctttgttttacct  CT-rich tract
                           ttattaatctcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaacaatatttctgacagtgatacttattcgtttaggaacttatgtaatgatgaaacagaagctcactcttattaatctctttgttttaccttgcagTGATTCTAGGCGAGGTAGCCAATTTTGCAGCATATGCATTTGCCCCTGCCGTACTTGTTACTCCTCTAGGAGCTCTAAGCATCATATTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT