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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG

Basic information

species Zea mays
transcript GRMZM2G079031_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 5
gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
|||||| | || ||| | || | |  |  || || ||   || |  | | |       |  |||        ||| ||   || |  |||  ||||||  |    | | || || ||  ||||||||||||||||||||||||| ||||||| |||||||||||||| ||||||||||||| ||||||||| | |||||||||||||||||||
gtatacttctagctgatgtgctgt--tttaagttgca--acgcctgatttt--gccattaaatt--------atactttatattatcctaatttaata--ttgtgattcctgtgcatttaattagACAAGAAGCTGCTGGTGCTCTGTGGAATCTGTCATTTGATGATAGAAACCGTGAAGGCATTGCTGCTGCGGGTGGCGTTGAAGCTTTG

upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0013g01430.t01 (Vitis vinifera), 3'ss of exon 5
gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
                 |||| | |    | | |       |    | | |  | || |  ||  || |  |||| ||   ||  ||||| |||  | |||  | |  |  |  ||   ||  || || |||||||||||||||||||||||  ||||||||||||| |||||  | ||||||||||| ||||  ||||| ||||| || |||
----------------attgacaagaat-agcatggtcttagcttgactttacaggcttctatattttcctaatattt---attcatcta-att--tgatttcacatattcacttac--aaacagGCAGGAAGCTGCTGGTGCTTTGTGGAATTTGTCATTTGATGATAGAAATAGAGAAGCCATTGCAGCAGCTGGTGGTGTTGAGGCCTTG

upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 6
gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatga-atctacattaataatt--caaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
                          |||||   | |    | ||||| |  |  |  | |||       ||||  ||   ||   ||||    | ||  ||  | |    | |    ||||||  || ||||||||||||||||| ||||||||  | |||||||||||||||||||| ||||| ||||| || |  ||||||||||| ||  ||
-------------------------atccaaaaacaacctagaccaag-cccatagattacataggaaa-gaatgttttagatagcatcttacctgattgttatccatgtatgttctcatcaaac-agGCAAGAAGCTGCTGGTGCATTGTGGAATTTATCATTTGATGACAGAAACCGCGAAGCAATTGCAGCTGCTGGTGGCGTTGAGGCCCTG

upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S13_130V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatacat-ataactgttttga-tatgctccaacttccatggcgtccaagtcttaatgcctgcattcttc-ctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
|||    | ||  |||    || | |||  ||       |||      | |   | ||  |    ||    ||   |   |  | |||   ||  ||  ||        |||  |  | |      ||||||||||| ||||| ||  ||||||| ||||| |||||||| |||||||| ||||| ||||| ||||  |||||||| || ||  ||
gtacgtgtgatctctgaggcgagtgtgcggcattgaaattggttggtcaatgagattggataaggtccaaactcggtgacttacctgacagtattttggtatc----ggctttcacatgtg----cagACAAGAAGCAGCTGGAGCACTGTGGAATCTGTCTTTTGATGATAGAAACCGAGAAGCTATTGCAGCAGCTGGTGGCGTGGAGGCACTG

upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S91_74V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatacatata-actgttttgatatgctccaa-----cttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaa-acttctatgtatcaaatt---agACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
|||| |  ||    ||   || |   |  ||        |   ||  || || |  |  |||       | |    | | || | |   |    |  |  | |  ||         |  || |      |   ||||||||||| || || || |||||||| ||||| || || ||||||||||| ||||| ||||| || |  |||||||| || ||  ||
gtatgcggatttgttggggtggtggacagcagggaggtgtttttgttgtgcaggggt-gatgtgaagggt-tgagggtagagatgggccggtgttctaagagtgttttgggcgtccccttggacggcgcttgcagACAAGAAGCAGCGGGAGCATTGTGGAATCTGTCGTTCGACGACAGAAACCGAGAAGCTATTGCAGCGGCTGGTGGCGTGGAGGCACTG

upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ24586 (Selaginella moellendorffii), 3'ss of exon 5
gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
                                                                          || |||  |   |  |  |  || ||  |     | | ||| ||    ||| |||||||||||||| ||  |||||||| |||||||||| |||||||| || || || ||||||||||  ||||| ||||| || |||
-----------------------------------------------------------------------gtgaggtcgtttcgtttcaagtctatcatggatttagtttgtgtttctt-ctagGCAAGAAGCTGCTGGCGCCCTGTGGAACTTGTCATTTGACGACAGAAATCGGGAGGCAATTGCTGCAGCTGGTGGTGTTGAGGCATTG

upper sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ24022 (Selaginella moellendorffii), 3'ss of exon 5
gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
                                                                          || |||  | | |  |  |  || ||  |     | |  || ||    ||| |||||||||||||| ||  | |||||| |||||||||| |||||||| || || || ||||||||||  ||||| ||||| || |||
-----------------------------------------------------------------------gtgaggtcgtttcatttcaagtctatcatggatttagtttgcgtctctt-ctagGCAAGAAGCTGCTGGCGCCCTTTGGAACTTGTCATTTGACGACAGAAATCGGGAGGCAATTGCTGCAGCTGGTGGTGTTGAGGCATTG

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|26559999|gb|CA832234.1|CA832234
EST:     GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAG                         ACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
genomic: GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAGgtatacatat ... atcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
EST: gi|87156811|gb|DY401600.1|DY401600
EST:     GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAG                         ACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
genomic: GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAGgtatacatat ... atcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
EST: gi|31354799|gb|CD439156.1|CD439156
EST:     GCCCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAG                         ACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
genomic: GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAGgtatacatat ... atcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
EST: gi|23357711|gb|BU645360.1|BU645360
EST:     GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAG                         ACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
genomic: GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAGgtatacatat ... atcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
EST: gi|50329592|gb|CO524718.1|CO524718
EST:     GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAG                         ACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG
genomic: GCTCTGGAGGCACTGGTGCAACTAACAAGTTCTCAAAACGAGGGTGTAAGgtatacatat ... atcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG
                    cattaat  putative branch site (score: 3)
              aatctacattaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacatataactgttttgatatgctccaacttccatggcgtccaagtcttaatgcctgcattcttcctgaatagttcgcatgaatctacattaataattcaaaacttctatgtatcaaattagACAAGAAGCTGCTGGTGCTTTGTGGAACCTGTCATTTGATGACAGAAACCGTGAAGCCATTGCTGCAGTGGGTGGCGTTGAAGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC