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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttatcccatatataaaggtatccaagatacttaggtgttttgagtgtctatgtactaaacatactgtgacatattattcttattggcacggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG

Basic information

species Glycine max
transcript GLYMA15G10030.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 15
------------atttatcccatatataaaggtatccaagatacttaggtgttttgagtgtcta-tgtactaaacatactgtgacatattattcttattggcacggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG
            |||| |  ||| | || |  |    | | |       | | ||  ||      ||   | || | |   |     |||||   |     || ||    ||||||||||||||||||||  ||||||||||||| |||||||| ||||||||||| ||  | |||||||||||||| || |||
gtttgacttttcatttttgacatgtgtacatttgcaaatgctgtcccattctcttaggtaaaagctgagttgaataaatatttttgcattatctgtggattcatgg----cagGTTGATGCTGCTATTGTCCGGATAATGAAGACGAGGAAAGTTCTTAGTCACACACTATTGATTACTGAACTCTTTCAGCAG
















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|22523750|gb|BU082561.1|BU082561
EST:     AGGAGAACACAAGCACCACTGAAAGAGTTTTCCAAGACCGTCAATATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|19934696|gb|BQ079726.1|BQ079726
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|6725094|gb|AW309493.1|AW309493
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|18734880|gb|BM528438.1|BM528438
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|58020712|gb|CX707454.1|CX707454
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|151404598|gb|EV274412.1|EV274412
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         -TTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|15812462|gb|BI784737.1|BI784737
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|209706055|gb|BW680825.1|BW680825
EST:     CGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: CGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|15814238|gb|BI786513.1|BI786513
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|209700820|gb|BW661251.1|BW661251
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|6567265|gb|AW234876.1|AW234876
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|58020885|gb|CX707627.1|CX707627
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|9902981|gb|BE611949.1|BE611949
EST:     AGGAGAACACAAGCACCACTGAAAGAGTTTTCCAAGACCGTCAATATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|9902896|gb|BE611864.1|BE611864
EST:     AGGAGAACACAAGCACCACTGAAAGAGTTTTCCAAGACCGTCAATATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|17401651|gb|BM178433.1|BM178433
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|58020543|gb|CX707285.1|CX707285
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|15204199|gb|BI426967.1|BI426967
EST:     AGGAGAACACAAGCACCACTGAAAGAGTTTTCCAAGACCGTCAATATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|151395410|gb|EV265287.1|EV265287
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         -TTGATGCTGCTATTGTGAGGATAATGAAGA
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGA
EST: gi|208316606|gb|GE117894.1|GE117894
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
EST: gi|17400275|gb|BM177057.1|BM177057
EST:     AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAG                         GTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC
genomic: AGGAGAACACAAGCACCACAGAAAGAGTTTTCCAAGACCGTCAGTATCAGgtcaattttc ... cggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctatgtactaaacatactgtgacatattattcttattggcacggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG
         tactaaa  putative branch site (score: 1)
                         acatattattcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttatcccatatataaaggtatccaagatacttaggtgttttgagtgtctatgtactaaacatactgtgacatattattcttattggcacggtttgcagGTTGATGCTGCTATTGTGAGGATAATGAAGACTAGGAAAGTGCTTAGTCACACGCTTCTTATTACTGAACTCTTCCAACAG

- - - - - - - - - - - - - - - - - -ggtgttt
- - - - - - - - - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catactg