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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacggcagcactatgttttcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG

Basic information

species Zea mays
transcript GRMZM2G007647_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 10
tgacggcagcactatgttttcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgat-tgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG
|||  |     ||        |   |  ||||   |  |  | |        |  |||||    |||  |||||| | |||  |||   |    | ||||||||||||| ||||| ||||||||||||||| |||||||| | || ||||| ||||||||||| |||
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccatt-caaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAG

upper sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 10
tgacggcagcactatgttttcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgat-tgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG----------------------------------
|||  |     ||        |   |  ||||   |  |  | |        |  |||||    |||  |||||| | |||  |||   |    | ||||||||||||| ||||| ||||||||||||||| |||||||| | || ||||| ||||||||||| |||                                  
tgaatgtttagctgaaccacaactgtcatttactcatttaatgcccatt-caaattattgtgggacttctgcatacttgataacttgccgcgattgtgcagCTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGGTATATTGAATTCTTTTTGTACTTTTCTTTCACC

upper sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 10
tgacggcagcactatgttttcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgattg---cagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG
  |  | |       ||||| |   ||  |   || |   || ||       || |  |  |  | | |||  |  |   |   |  |      |||   ||||||||||||||| | ||||||||||||||| |||| || || ||||| ||||||||||| || |||
--aaagtatttgctagttttga-aatgtctgccctgatgacttcagattgacagatcctttattatttttgatttttaactaattggtatgcttttgaaccagCTTACTGGAGATTTGGACAAGATGGTTGCATTACAGAGATTGTTAGAACCATATGGCATTTGTGAG

upper sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 10
--------tgacggcagcactatgttt-tcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG
        ||   |       |||| |  |||| ||  |  ||  | ||   ||     ||   ||||   ||  | ||   |||| |||    | ||||      ||||||||||||||| | ||||||||||||||| | || || || ||||| ||||||||||| || |||
aaagtatttgctagtttggaaatgtctgccatgatgact--tcagattgg--cagatccttcattattttcaa-tttttatctaattgatatgatcttgaac----cagCTTACTGGAGATTTGGACAAGATGGTTGCATTGCAGAGATTGTTAGAACCATATGGCATTTGTGAG

upper sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 10
tgacggcagcactatgttttcatgc-tgctttatctaactgctccaagcgattagctattgcaa---aactcttgcataatggatcccttattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG
  |       |  | | |  | ||  |  |  |||| | |    | |    || ||| |||         | |||        ||   ||     ||  |  |||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||||| || || |||
-aaaaaatatatgaagctgacttggattttccatcttaat--ctctatttttttgcttttgtgttttggattttgtgctg-aaatttgttggctgtgggtatagCTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAG

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|6448417|gb|AW181183.1|AW181183
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|60356357|gb|DN223330.1|DN223330
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|22521063|gb|BU079874.1|BU079874
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|44900488|gb|CK827033.1|CK827033
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|4827621|gb|AI668313.1|AI668313
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|50337798|gb|CO532924.1|CO532924
EST:     GAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: GAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|87156533|gb|DY401322.1|DY401322
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|211044763|gb|FL481858.1|FL481858
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|37374784|gb|CF623779.1|CF623779
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|67022242|gb|CO450991.1|CO450991
EST:     TCTTNCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACANAGGTTATTAAAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|67017113|gb|CO445862.1|CO445862
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
EST: gi|89247462|gb|DY619248.1|DY619248
EST:     TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAG                         CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA
genomic: TCTTCCGAGCAAAACCTATTGACGTTTCTGACCATACAGTAACCCTTCAGgttcgcttcc ... atgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgattagctattgcaaaactcttgcataatggatcccttattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG
                                        tattgat  putative branch site (score: 3)
                                       ttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacggcagcactatgttttcatgctgctttatctaactgctccaagcgattagctattgcaaaactcttgcataatggatcccttattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -cggcagc
- - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - -ctgctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgca