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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctggtcaatatatcacaaagttttatggtttattctgcttatcggtgtaaatttattacatctggttgtttctcatgcccctttgttctgtccatacgaatgaagtagttttggttttaatctccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT

Basic information

species Zea mays
transcript GRMZM2G052750_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 19
gttctggtcaatatatcacaaagttttatggtttattctgcttatcggtgtaaatttattacatctggttgtttctcatgcccctttgttctgtccatacgaatgaagtagttttggttttaatct-ccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                                                             || ||        |  |  |   |||  |  | | |    || | |||| ||||| | |||  || |||| || | || | |||||||||||||||| |||||||| || || |||||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| || |||||||| ||||
-----------------------------------------------------------------------cactcaatacctgagcaaccaatataccagaacaatctcgctgatattattatctgccttggatctttgttctcatttataatt-gatattctgatgacagCTTCAAATGGACACTCTTCAAAGTCGGCTTGATGCTGAGTTCCTTCTTGCTCACATGTGTTCTGTCAAGTTTAAGGAATGGATTGTTGTGCTAGCAACTT

upper sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 20
gttctggtcaatatatcacaaagttttatggtttattctgcttatcggtgtaaatttattacatctggttgtttctcatgcccctttgttctgtccatacgaatgaagtagttttggttttaatctccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                                        ||| |  |   ||  |   ||||    |       |||| | |    ||  |   ||||  ||||   |||||      ||||| | ||  ||  ||||| |||        ||||| |||||||  ||| | || || ||  | ||||| || || || ||| |||||||||| || |||||||||||||||||||| || || || |||||| 
------------------------------------------------------gctataatgtaaagtcttaaatcatttggcaggagcttgtctacatttgtgctgatattttctttttg--ctcct------ttattgaacac-tattttttgttat--------cagCTTCAAATGGGAACATTACAGAGCCGTTTGGATGCTGACTTTCTCCTATCTCATATGTGCTCTGTCAAGTTTAAGGAATGGATAGTTGTCCTGGCTACTC

upper sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 19
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 20
gttctggtcaatatatcacaaagttttatggtttattctgcttatcggtgtaaatttattacatctggttgtttctcatgcccctttgttctgtccatacgaatgaagtagttttggttttaatctccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                                                       ||| | ||     ||||   | |  |  | |        |||    | ||  | |  ||||   ||||||   || |   || | || |  |  |  |||||  |||||| ||| ||||| || || || ||||||||||||||| | ||||||||||| || || |||||||| || ||||| || || || |||||| 
--------------------------------------------------------------------agatttttgataaat-tttggagtattgaggcaagcatgactgttaatttctttttttttttgacctttatttg--atttgatttattgtttcatattttcagCTTGAAATGGGTACGCTGCAGAGCCGGCTGGATGCAGAGTTCCTTTTGGCTCATATGTGCTCTGTTAAGTTTAAAGAGTGGATAGTTGTCCTGGCTACTC

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|87152673|gb|DY397462.1|DY397462
EST:     CTGCTCGTCTAGAGAATTTTGCTTCCGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|211446884|gb|FL341663.1|FL341663
EST:     CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|211446492|gb|FK979151.1|FK979151
EST:     CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32867742|gb|CF007424.1|CF007424
EST:     CTGCTCGTCTAGAGAATTTTGCTTCCGCGCTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|211253319|gb|FL352230.1|FL352230
EST:     CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
EST: gi|32868501|gb|CF008183.1|CF008183
EST:     CTGCTCGTCTAGAGAATTTTGCTTCCGCGCTCGAACTGATTGGACAAAAG                         CTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT
genomic: CTGCTCGTCTAGAGAATTTTGCTTCTGCACTCGAACTGATTGGACAAAAGgttctggtca ... ctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttaatctccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT
                                           ttctgat  putative branch site (score: 3)
            ttgaaacttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctggtcaatatatcacaaagttttatggtttattctgcttatcggtgtaaatttattacatctggttgtttctcatgcccctttgttctgtccatacgaatgaagtagttttggttttaatctccttgaaacttatttatcatgtacattttggtattctgatgacagCTCCAAATGGATACACTGCAAAGTCGACTTGATGCAGAGTTCCTTCTAGCTCATATGTGTTCAGTCAAGTTTAAGGAATGGATCGTGGTGCTAGCTACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA