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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggatagtatgtgttgtttcccacttgaatttatgtaaattcataaatcataacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA

Basic information

species Glycine max
transcript GLYMA08G37270.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggatagtatgtgttgtttcccacttgaatttatgtaaattcataaatcataacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA
                                                  |||      |||   |     |  || |   ||| | ||||||   ||  |||   |  ||  |||  || |  |      |||  |     |   | | |  ||||  ||||||| |  || |||||||||||    ||||| || ||||| ||||||||||| ||||| ||||| || |||||||| || ||||||||| | |
--------------------------------------------------gtatggcatgatgaaaacgataaaaa-aaactagcaggtgttgaa-cctgcttct-tgcattaaaaaccaaaggtt----tagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
---gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggata-gtatgtgttgtttccca-cttgaatttatgtaaattcataaatca-taacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA
        ||  ||||||||  |  ||| |  ||     ||  |    |  |     | ||  | | ||||    |    ||  |  |  | | ||||| |  | |||||  |||| |   |  |      | ||||| || | ||| | |  || ||||||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||||||||| ||||| ||| |||| ||||||||||| ||||
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactt-tatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
---gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaac-aggatagtatgtgttgtttccc-------acttgaatttatgtaaattcataaatca-taacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA
        ||  ||||||||  |  ||| |  ||     ||  |    |  |     | ||| | | ||||   ||  |  |||  ||| | || |  ||          ||||||  |||| |   |  |      | ||||| || | ||| | |  || ||||||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||||||||| ||||| ||| |||| ||||||||||| ||||
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactt-tatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 1
gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggatagtatgtgttgtttccca-cttgaatttatgtaaattcataaatca-taacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA
                                                        |||    |  || | |   |   |   |  | | ||||| |  | |||||  |||| |   |  |      | ||||| || | ||| | |  || ||||||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||| ||| ||||||||| ||||| ||| |||| ||||||||||| ||||
--------------------------------------------------------tcactactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactt-tatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 9
gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggatagtatgtgttgtt-tcccacttgaatttatgtaaattcataaatca-taacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA
                                                        |||    |  || | |   |   |   |  | | ||| | |   ||||||  |||| |   |  ||     | ||||| || | ||| | |  || ||||||| ||||||||||| |||||||||||||| || ||||| || |||||||| ||| ||| ||||||||| ||||| ||| |||| ||||||||||| ||||
--------------------------------------------------------tcactactatttattaggcaagtgtctgcttcttttgctattgaacttgaggttatattgttggatgtggaactaacatttatactt-tatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

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|20813250|gb|BQ297728.1|BQ297728
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|6134799|gb|AW133192.1|AW133192
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|9900480|gb|BE609448.1|BE609448
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|120496684|gb|EH224851.1|EH224851
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|213588396|gb|DB967882.1|DB967882
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|9439993|gb|BE440504.1|BE440504
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|120496962|gb|EH225129.1|EH225129
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|17518985|gb|BM188027.1|BM188027
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|17400278|gb|BM177060.1|BM177060
EST:     GATATTCTACAGAAAAGGGGTTAAAGAAATTAACAATCAATTGTAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACT
genomic: GATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAA-GGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACT
EST: gi|22524932|gb|BU083743.1|BU083743
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAG                         GTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
EST: gi|22539787|gb|BU089630.1|BU089630
EST:     TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACACACAGGGAAGAGAT                         GTATTGTATGACTACGACGACAGAATCGACCGAGCTGTT
genomic: TGATATTCTACAGAAAAGGGGTTAAAGAAATTAACAAACAAGGAAAAGAGgtcaattcca ... caatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaatttatgtaaattcataaatcataacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA
                        tcataac  putative branch site (score: 2)
                                    ttcttctttcaattt  putative PPT
     atttatgtaaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggatagtatgtgttgtttcccacttgaatttatgtaaattcataaatcataacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT