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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

aTCACTTGAACTTGCTCAAGAAAATGCTGCTGATCTGGAG

Basic information

species Zea mays
transcript GRMZM2G113640_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113640_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------------------------------------------------------------aTCACTTGAACTTGCTCAAGAAAATGCTGCTGATCTGGAG
                                                                                                                                  ||| |||||||||||||||||||||||||| ||||| |||
caagaaaatgaggttcatcactcagtatctttatgccttttgttgttatttgttcagttacaatttctaatcttatgtccctttggttgtgaaatcacagGCATGTTGTTGGAATTGATATTGACCCGCAATCCCTTGAACTTGCTCAAGAAAATGCTGCAGATCTAGAG
















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|211270654|gb|FL248444.1|FL248444
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270654|gb|FL248444.1|FL248444
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|71438832|gb|DR819882.1|DR819882
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|71438832|gb|DR819882.1|DR819882
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270652|gb|FL248442.1|FL248442
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270652|gb|FL248442.1|FL248442
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270657|gb|FL248447.1|FL248447
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270657|gb|FL248447.1|FL248447
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270656|gb|FL248446.1|FL248446
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270656|gb|FL248446.1|FL248446
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|76012002|gb|DT939172.1|DT939172
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|76012002|gb|DT939172.1|DT939172
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270651|gb|FL248441.1|FL248441
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270651|gb|FL248441.1|FL248441
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270648|gb|FL248438.1|FL248438
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270648|gb|FL248438.1|FL248438
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|6227108|gb|AW155812.1|AW155812
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACAG                         TCACTTGAACTTGCTCAAGAAAATGCTGCTGATCTGGAG
genomic: ACATGTTCTTGGTATTGATATTGACCCGAC-Ta ... aTCACTTGAACTTGCTCAAGAAAATGCTGCTGATCTGGAGgtatgacaat ... gat
EST: gi|50327796|gb|CO522922.1|CO522922
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|50327796|gb|CO522922.1|CO522922
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270649|gb|FL248439.1|FL248439
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270649|gb|FL248439.1|FL248439
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270646|gb|FL248436.1|FL248436
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270646|gb|FL248436.1|FL248436
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270655|gb|FL248445.1|FL248445
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT
EST: gi|211270655|gb|FL248445.1|FL248445
EST:     ACATGTTCTTGGTATTGATATTGACCC-ACA                         G
genomic: ACATGTTCTTGGTATTGATATTGACCCGACTa ... a-a ... aTCACTTGAACT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aTCACTTGAACTTGCTCAAGAAAATGCTGCTGATCTGGAG

- - - - - - - -  AAGAAA
- - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - TGCTGC
- - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - GCTGAT