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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcatctttcttgccaaagatattgcacccttttgcttcaccatattcttacattcattcattgtcttctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC

Basic information

species Zea mays
transcript GRMZM2G160842_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 3'ss of exon 7
gtaggcatctttcttgccaaagatattgcacccttttgcttcaccatattctta---cattcattcattgtcttctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC---------
|||    || ||  | |  |  || || ||  ||| |  |||||  |||||||     |||||| || || |||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| || |||| ||||||||| |||||||||||||||||||||||||||||||| || |         
gtaaatctcattactcctgataatctt-cattcttgtagttcactttattctttttttattcatgcactgacttctctaacagttgactgtttatcatcataatggaagTCCATGCTATCGATGCCTTTTCCCAAATCCACCACCAGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGAGTTCTTGGGGTTG

upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G46300.1 (Glycine max), 3'ss of exon 7
-----------------------------------------gtaggcatcttt---cttgccaaaga-tattgcaccctt--ttgcttcaccatattcttacattcatt-cattgtcttctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC
                                           | || || |    || | |||  | |   ||   |||  ||   ||||   |||     ||| | | |     ||| |    ||| | ||||| ||  || | |||||  | || |||||||||||||||||||||||||||||||||    |||| ||||| || ||  | ||  |||| || |
gtatatgtctaaatatttgtttttctagcatttaagttaactaatgcttcatggagctcgacaagtactcccgcgtacttgattatatcacataatttgaggattaactacggaaacttatgctgcagCTTACTGTCTACAATTACAATGGTGGTCCTTGCTATCGGTGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTC

upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G02410.1 (Glycine max), 3'ss of exon 6
-------------------------------------gtaggcatctttcttgccaaagatattgcacccttttgcttcaccatattcttacattc----attcattgt-----cttctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC
                                       |   ||  ||| |         | | | ||  | ||||| |  ||||      |||     ||| | | |     ||| |    ||| | ||||| ||  || | |||||  | || |||||||| ||||||||||||||||||||||||    |||| ||||| || ||  | ||  |||| || |
gtatatgtctaattattttttttcccagcatttaagttgaataatgcttcatagagcgacaagtactcctgtgtgcttgattatatcacataatttgaggattaactatggaaacttttactgcagCTTACTGTCTACAATTACAATGGTGGTCCTTGCTATCGATGCCTCTTTCCAACTCCACCACCTAGAACAGCATGCCAAAGTTGTGCTGAGGGTGGAGTTC

upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0090g01020.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------gtaggcatctttcttgc---caaagatattgcacccttttgcttcaccatattctt------acattcat------------tcattgtcttctcta-acagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC
                                                 |||  || | |  ||     || |  || | |    |   ||||| ||| || |       | | ||||            ||||    || | |  | || | ||||||||  || | || ||| | ||||||||||||||||| ||||| |||||||||||     |||| || || ||||| ||||| ||||| ||  
gtatgttatgcatctgctttcatattctgttattcttgtgttacacctataga-atttcttatgtgaataagggaatgggaagtgtaatcttcatcattttttgttgtggaaactcatagcataactgcatcatgaaattttttgtatagCTCACTGTTTACAATTACAAAGGAGGTCCATGCTATCGGTGCCTTTTTCCTACTCCACCACCAACAACAGCATGTCAAAGATGTTCAGATAGTGGAGTTT

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|60352218|gb|DN219191.1|DN219191
EST:     GGCTTAGAAGGGCAG                         TTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCA
genomic: GGCTTAGAAGGGCAGgtaggcatct ... tctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCA
EST: gi|78106504|gb|DV524922.1|DV524922
EST:     CCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG                         TTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCA
genomic: CCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAGgtaggcatct ... tctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcacccttttgcttcaccatattcttacattcattcattgtcttctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC
                       ttcttac  putative branch site (score: 2)
                                   ttcattgtcttctct  putative PPT
                    atattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcatctttcttgccaaagatattgcacccttttgcttcaccatattcttacattcattcattgtcttctctaacagTTGACTGTTTATCATCATAATGGAAGCCCATGCTATCGGTGCCTCTTTCCAACTCCACCACCTGTGGCAGCCTGCCAGAGATGCTCAGACAGTGGTGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG