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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgccaatcgttagtttttttgggtaaaatacactggcggtccttaaacttgtagctttgtattatcctggtccttttaactcataaattgcac...

Basic information

species Zea mays
transcript GRMZM2G107696_T02
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os01g08200.1 (Oryza sativa), 5'ss of exon 15
ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgccaatcgttagttttt----ttgggtaaaatacactggcggtccttaaacttgtagctttgtattatcctggtccttttaactcataaattgcac
|||| ||  ||||||||||||||| |||||||||| | || ||||||||||||||  |||||||||| |||||||| ||||||||||||||| ||||||    |  |||| ||||    |||   | | |   | |   | | ||   ||    ||    |||| |    |                       
ATGTATACGTAGATGTGCCAGATATAATTGATATCTCGCACATGCGCAGCAAAGGCATACAGCCTGGTGAAGAGCTACTACCTGAAGGAGgttagactgttgtttattagattttcaacttgatcagattttcccgattgactttg--ctgactgcaacatattcttgcag-----------------------
















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|116817395|gb|EC860237.1|EC860237
EST:     TATGCGCAGC-AAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAG                         GTTCTGGATGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGAT
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGG-TGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGAT
EST: gi|211494928|gb|FL217185.1|FL217185
EST:     TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAG                         GTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAA-ATT
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGAT-
EST: gi|116819768|gb|EC862916.1|EC862916
EST:     TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAG                         GTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
EST: gi|31361116|gb|CD445473.1|CD445473
EST:     TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAG                         GTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
EST: gi|149014867|gb|EE044578.2|EE044578
EST:     TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAG                         GTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
EST: gi|71595705|gb|DR906456.1|DR906456
EST:     TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACTTGAAGGAG                         GTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
EST: gi|44682206|gb|CK787254.1|CK787254
EST:     TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAG                         GTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA
genomic: TATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgc ... tacactttagGTTCTGGTGACGACAGTGCCGAGCCTGCTAATCCTGTTGCCAGTGAGGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTTATATAGATGTGCCAGATACAATTGATATCACACATATGCGCAGCAAAGGATTACAGCCTGGGGAAGAGCTGCTACCTGAAGGAGgtcagactgccaatcgttagtttttttgggtaaaatacactggcggtccttaaacttgtagctttgtattatcctggtccttttaactcataaattgcac

- - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG