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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaataatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA

Basic information

species Zea mays
transcript GRMZM2G153945_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153945_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 6
-ctaa--taatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA
  |||  |||| | ||    || |         ||| |  ||||  | ||||| ||||||       |  | ||   | |  | |   |   | || || ||| ||||| |||||||| ||  ||||||||||||||||||| ||||||||||| ||||| ||| | ||||||||||| ||||| |||||||| || ||||| 
tttaaattaatttgtttctcatctcatctcttttgactcctttgagattttat-tttgttttattgattcttagcttcttctgtg--ttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACC

upper sequence: GRMZM2G153945_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
-ctaa--taatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA
  |||  |||| | ||    || |    |    ||  |  ||||  | || || ||||||       |  | ||   | |  | |   |   | || || ||| ||||| |||||||| ||  ||||||||||||||||||| ||||||||||| || || ||| | |||||||||||||| || |||||||| || ||||| 
tttaaattaatttgtttctcatctcatcccttttgcctcctttgagatttgat-tttgttttattgattcttagcttcttctgtg--ttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC

upper sequence: GRMZM2G153945_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 3
ctaataatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatct--attatacattt---------cagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA
                          |  ||||||| ||  ||| |     ||  |  | ||        | |  |  | ||||    | | |||||||         ||||||||| |||||||| |||||||| || || |||||||| ||||||||||| || || ||||| |||||  | ||||| |||||||| || |||||||| 
--------------------------gtaatgaatgcttctgaaataatagttgatcacacagtattcttgaggaaggaaagattgtaactgtacattttcgctgttgcagGTATGCGATGACTGGTCAACTGACACAGAAGAGTGATGTTTATAGTTTTGGTGTGGTGCTTTTGGAGCTCTTGACTGGTAGGAAACCCGTCGATCATACG

upper sequence: GRMZM2G153945_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
ctaataatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttc---agGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA
  ||| ||   ||   |  |||  |     |      | |   | |  ||   |    |    |||||   | ||||  |   | | | | ||  |||   |||||||| |||||||| ||| ||||||| || |||||||| ||||||||||| ||||| || ||||||||||| ||||| || |||||||| |||||||| 
aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgat---tcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC

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|71756905|gb|DR954842.1|DR954842
EST:     CGTCTACATTCTACTCGTGTCCTTGGAACCTTCGGATATCATGCTCCAGA                         GTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGG
genomic: CGTCTACATTCTACTCGTGTCCTTGGAACCTTCGGATATCATGCTCCAGAgtaattattt ... tacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGG
EST: gi|148929739|gb|EC876646.2|EC876646
EST:     CGTCTACATTCTACTCGTGTCCTTGGAACCTTCGGATATCATGCTCCAGA                         GTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGG
genomic: CGTCTACATTCTACTCGTGTCCTTGGAACCTTCGGATATCATGCTCCAGAgtaattattt ... tacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctttgttcctcatctgatcagtgacataagagatctattatacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA
                atctgat  putative branch site (score: 4)
                                     atctattatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaataatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttcagGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA