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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctatcgtgtctattgaaaagcttttcctagttcagctcgatttggtgatattttatgattgtgtggatcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG

Basic information

species Zea mays
transcript GRMZM2G063792_T06
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 8
gtatctatcgtgtctattgaaaagcttttcctagttcagctcgatt-tggtgatattttatgattgtg-tgg-----atcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
|||| | || || ||| || ||||| || |||   |||||  |||| ||||     |||| |||||   |||      |  |||||||||| ||||||||||||||| |||||||| ||||||||||||||||| || |||||||| ||||||
gtatttgtcttgcctagtgcaaagccttccctg--tcagcgtgattatggtttatgtttacgattggaatggctgttgttctgttcagGACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 7
------------------------------------------gtatctatcgtgtc-tattgaaaagcttttcctagttcagctcgatttggtgatattttatgattgtgtggatcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
                                          |||  |||  |||  || |   ||    |      |      | |  ||   ||| || ||  | |    | | ||||  ||||| ||| ||||| || ||||||||||| |||||||| |||||||| || |||||  | ||||| 
gtacataaatattcagtaaaaatgctacgagtttttaattgggtacatatgctgttatacttccaaaacatggtgtttatgatgccaactga--atacttgatattggcaatggttttgt--agGACTTGGGTGGAGCTATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------------------------------------------------------gtatctatcgtgtctattgaaaagcttttcctagttcagctcgatttggtgatattttatgattgtgtggat-cttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
                                                                                            | | |  |        |  |           |  || ||   ||| ||||   | | | || | |  ||  || |  ||| | |||||||||||| ||||||||||| ||||||||||| |||||  | || ||| | ||||||
gtatgccatcaaatatctgccattgtttttctgttgtcatgagtcagtatggtgttctaccattctttcaaattagttggccagatcacaggtttcttttaatgcccaaggaagacaagtggatatagttc--cttgctgatgaat-acgctttttttcatgtttatgtagGGCTTGGATGGAGTTATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 8
--gtatctat-cgtgtctattgaaaagcttttcctagttcagctcgatttggtgatattttatgattgtgtggatcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
  || | |||  ||  || |     | | ||  || | | |   |  ||  | | |  |   ||      |   | || |||||| | |||||||||||| |||||||| || ||||| |||||||||||  | || || || ||  ||
gtgtgtttatatgttcctttctgttatcattgacttgctta---catttcagcggtcctcagtgtcatcatatttgtttttcagGGCTTGGATGGAGTTATCCATGTGACATGTGGAGCGTTGGTTGTATATTGGTGGAACTATGTTCG

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|32804365|gb|CD956601.1|CD956601
EST:     GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTTTATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|33104273|gb|CF064233.1|CF064233
EST:     GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|32804851|gb|CD957087.1|CD957087
EST:     GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|60345282|gb|DN212255.1|DN212255
EST:     GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|213175408|gb|FM189251.1|FM189251
EST:     GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|60398865|gb|DN231681.1|DN231681
EST:     GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|32802406|gb|CD954642.1|CD954642
EST:     TAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGG                         GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTGGTATCGACGAGGCACTATCGGGCTCCAGAAGTTATATTGGgtatctatcg ... tcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctagttcagctcgatttggtgatattttatgattgtgtggatcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
                                             tcttgttc  CT-rich tract
                       tgatattttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctatcgtgtctattgaaaagcttttcctagttcagctcgatttggtgatattttatgattgtgtggatcttgttcagGACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT