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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgttatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 12
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaa-gctgat-ataatttgatcatgt-----tatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                   |||| ||  | |   |   |  |   ||| ||  | |      | |    |  ||  |||||||  |   |      |     ||||| | |||| |||| |||   |||      | | |  | ||  |||||||||||||||||||||||||||| ||| |||||||  | ||||||||||||||||||
-----------------------------------gtat-atactttgcgtgccttctttagtg-tgcttcaacaaatataggccgcttatcttttgaaagagcttgtgagatccgctcttaatggtgatgataacttggaaatgcatcaatgttttgtcatgaaacagGGCCAGATCAAGACTGGAGCTCCTTGCAGATCTGAGCGCCTTGCCAAGTACAACCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 3'ss of exon 15
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgt-tatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                                |   |||||   |      |    ||     || |||  |   ||  || || |   || ||  | ||    | |     |      |||  || | | ||||||| |  ||||||| ||||||||||||||||| ||||||||||| ||  | |||||||| |||||||||
-----------------------------------------------gtaagattctgtgctctacattcactgtagtgaacttta-cggcatcctgtatta--gttgttactcttgtactgaat--gtgagggctgaatatatctttgtcattctgaaacagGGTCAGATCAAGACTGGAGCACCCTGCCGATCAGAGCGCCTTGCCAAATACAACCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G446253_T01 (Zea mays), 3'ss of exon 14
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgttatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                                                ||    | |  ||        |   |||  |  | |  ||| |    |      |||  |   || | |  || |  |   ||| | |  |||  |||||||| |||||||| |||||||||||||| |||||  | || ||||| |||||||||
----------------------------------------------------------------gtacgctgtcagctgg----cgcacaaacatatactgtcgaat----tgaacgtcttgggggtat-tgacctggt--ttccatgacttggttt--cagGGCCAAATCAAGACAGGAGCTCCCTGCCGGTCTGAGCGCCTGGCCAAATACAACCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G048371_T01 (Zea mays), 3'ss of exon 16
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataa---cgattcttttttttaccttaagctg--atataatttg--atcatgttatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
||| | | |                |    ||      |     || ||    ||||               ||     |  ||| || ||  | | |  ||   | |   ||| ||| ||  ||||  |   ||| || ||   |  |||| | |  |||| |||||||| ||||| ||||||||||| |||||| |||| ||  | |||||||| |||||||||
gtatgatttactttctgtgcatatctaggatagagaagtttcaatcattcctgttctgaaaacatgagacagtgccttcatatttctcaaaggtcttagcaaattcaaacttttatttgactgtaaggcgtagtatcatctgtctttttgttttctttttatataacagGGTCAGATTAAGACTGGAGCACCCTGCAGATCAGAGCGTCTTGCCAAATACAACCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 15
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgt-tatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                                    |   ||   || || || |||     | |||| | |    || || | | |             | || ||| |||||| |  |||| |||| |   | ||     |||||||||||||||||||||||||||| ||| | |||||| | |||||||| || ||||||
-------------------------------------------------aataaaattgtagtagtatcatatttaagagattt-gacagttttctggacagc-------------atctcaagttgatatgacctgatgatgtgtgccttatatgcaaacagGGCCAGATCAAGACTGGAGCTCCTTGCAGGTCTGAACGCCTTGCCAAATATAACCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S133_85V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttccc-gtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataat---ttgatcatgttatgtca----------------ttatttaa-----cagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
       ||||  ||       |  |||| || |  | |  |||| | |||  || | |    |  | | |  ||| | ||| ||   |  ||||||   |     ||  |  ||| |||||||  | ||||  |   |||    || | ||                   |   || |     ||||||||||| |||||||||||||| ||||| ||||| ||  |  ||||||||||||||
---gtacgtcagcatttttttttactttcttagttatgttgtgttttgttttgttttactttattttatttcttggacaaaaatt--ccggaatttt--ttcgtagttgatgctttgaccttaaattaatatcgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatgatgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ14601 (Selaginella moellendorffii), 3'ss of exon 12
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgttatgtcattattta-acagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                                                                                   |||  |       ||| |  | |   ||||    ||||||   ||| |||  || |||   ||||| ||||||||||| |||||||| ||||||||||| |||||||| || ||||| |||
--------------------------------------------------------------------------------------------------gtaagaacagaaaatttcatatgag--tgat---ctttgat---gttttgtttttgtttttgcagGGTCAGATCAAGACGGGAGCTCCATGCCGATCTGAGAGGCTTGCGAAATACAATCAG

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|58014968|gb|CX701710.1|CX701710
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254343119|gb|GR859281.1|GR859281
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|9258535|gb|BE346682.1|BE346682
EST:     GGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|57574275|gb|CX547250.1|CX547250
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254320423|gb|GR826872.1|GR826872
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254335782|gb|GR847310.1|GR847310
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|10254318|gb|BE822084.1|BE822084
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|16343634|gb|BI969229.1|BI969229
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|7588392|gb|AW704189.1|AW704189
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254329397|gb|GR838950.1|GR838950
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|58020394|gb|CX707136.1|CX707136
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|213597412|gb|DB977775.1|DB977775
EST:     TGAAACTGAGGATACCTTCATTGCTGACCTATCAGTCTCGA-TAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: TGAAACTGAGGATACCTTCATTGCTGACCTATCAGT-TGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|151408704|gb|EV278512.1|EV278512
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254317871|gb|GR832039.1|GR832039
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|17963567|gb|BM270314.1|BM270314
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
EST: gi|254329396|gb|GR838949.1|GR838949
EST:     GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACT                         GGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC
genomic: GTGAAACTGAGGATACCTTCATTGCTGACCTATCAGTTGGATTAGCAACTgtaagttgtc ... tatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttttaccttaagctgatataatttgatcatgttatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
                                    ttatgtcattatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttcccgtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataatttgatcatgttatgtcattatttaacagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT