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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctttactagtactcaatctttggttcttggacatggcatagactatataggggtaagtgtttgacagatttttcattgtgtgtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCT

Basic information

species Glycine max
transcript GLYMA07G02630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G02630.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
-----------------------------gtaagtctctttactagtactcaatctttggttcttggacatggcatagactatataggggtaagtgtttgacagatttttcattgtgtgtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCT
                             |    |||| || |  || |  ||   ||   |  |     |     |  |||     |  ||| |  || |     || |     ||  |   | ||| | || |||||||| |||||||||||||| ||||| || ||||| ||||  || ||||| || || ||||| || ||||  ||||| ||||||||   ||
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaac--ttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT

upper sequence: GLYMA07G02630.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtctc---tttactagtactcaat--ctttggttcttggacatggcatagactatatagg-ggtaagtgtttgacagatttttcattgtgtgtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCT
|||||||        || | || |      |||||||   |     ||    | || ||   |   || | || | ||  ||    |   | | |||  || ||| | || || ||||||||||| |||||||||||||| |||||||| |||||||| ||||| | ||| ||||| || ||||| |||||||||||||||||||
gtaagtccaaaacccacaaataattggcgactttggtggattattctg-tgaacaccatccggatagtgaatgatcgatcgagcaatttctttatgtt-ttacagGTGGTGAAGGATGGATACCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCT
















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|21993658|gb|BQ785186.1|BQ785186
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACC
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACC
EST: gi|213597737|gb|DB964474.1|DB964474
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGG
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGG
EST: gi|151404463|gb|EV274277.1|EV274277
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
EST: gi|213611520|gb|DB960800.1|DB960800
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGNAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
EST: gi|10234233|gb|BE803121.1|BE803121
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
EST: gi|7029221|gb|AW459004.1|AW459004
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
EST: gi|192306949|gb|FG999968.1|FG999968
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
EST: gi|209713520|gb|BW681521.1|BW681521
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGA
EST: gi|209712903|gb|BW679180.1|BW679180
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAA
EST: gi|21993790|gb|BQ785318.1|BQ785318
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
EST: gi|192296121|gb|FG989481.1|FG989481
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTT                         ATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAAGCATCTGATACTAGCCTTgtaagtctct ... gtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagactatataggggtaagtgtttgacagatttttcattgtgtgtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCT
                      gtttgac  putative branch site (score: 4)
                               atttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctctttactagtactcaatctttggttcttggacatggcatagactatataggggtaagtgtttgacagatttttcattgtgtgtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA