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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaacctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG

Basic information

species Glycine max
transcript GLYMA12G31980.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaacctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
                       |   | |||  | || | |  | ||  |       |||  ||    || || |  |   |  ||||| |    |   || ||||    || |  |||    |       ||   | | | |||  ||| |    |  | | | |||| |||||||||||||||||||||||||| |  || || |||||||||||||| || ||||||   ||||||||||||||||||||| | || ||||| |
-----------------------gtaatattctgc-ttatgtggtttacgaagaa---ctagctgctccattacctttttgaac-tcatgttggagtactttcgaagtttgaacttcataccttattgc---tgtgcctaatgtcagtcctgtccact--tctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG

upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctc-tacttgaataatcacttgataagatatcatgg-tcacatttatttgaaggaaaaattaaataaaaaaaa-agaaatgcaacaagtttcaaacctctgttttgattt-------ttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
                                                   |  | |    |||||  ||||  |||  |    | |||||| ||  ||||||     |      |    || ||  |   | ||||| |       |     | | || || | |       ||||||||||||||||||||||||||| | | || |  || || |||||||||||||| || ||||||   || |||||||| ||||| ||| | || |||||||
--------------------------------------------------gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG

upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007185_T01 (Zea mays), 3'ss of exon 6
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaaca--agtttcaaacctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
                                                                   |  | ||  |||   ||||   |     | ||  |||  |  |  ||||  |   | |       |   ||   |  || |  | | ||   |    ||  |||||||||||||||||||||||||  ||||||  || || | |||||||||||| || ||||||   |||||||||||| |||||||| | || ||||| |
-------------------------------------------------------------------ttcttacaagatcc-atatatggactgtagtt--ttggggtcattattactttctacatgttttttttcactctaactttagtcatgtgcactcggattgtagGATCATGTTGAAGGATACCTTGAGCTGTCAGGGAAAACCAGGACATACTTTGCAACAGCTGTTGCTTTATGGGATGCTAACTTCTATGTGAAGGTTGACG

upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 5
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaac--ctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
                                                | | ||   ||    |   |  |     |    |||| ||||   || ||| ||   ||      | | |          |   | |  ||  ||   |    ||    |||  || ||||||||||||||||||| ||||||| ||||||||  || || ||||| |||||||| || ||||||    ||||||| || ||||| ||| | || ||||| |
-----------------------------------------------gtaagttaattccttgttgctcttgcgcaggagtgata-catgtgaac-tttgttctgagttttgctcagacggctgg---gttttcctccatattcacagtggctacaatttttttgttcagGATCATGTTGAAGGGTACCTTGCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACG

upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 6
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaacctctgtt-ttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
             |  |  | ||| | | |||  |  || ||    |    | |   |||   ||  | ||  ||  |    | ||| |  | || | || ||      ||| |||| |             |||  ||     ||   || ||||  ||  |   ||||| ||||||||||| ||||| ||| |||| || |||||||||| ||| ||||| |||||||||   || |||||||| || ||||| || ||||||||||
------------gtaatggttttg-tatcttcttctgtgacttgctttctgtattcttctgtatgcttgatgcctccaaggaacatcttcattacctataatta----taaagttaatt-------------tgcccca-----catgtctgtgttactgtgtgagcagGAACATGTTGAAGGTTACCTCGAACTGTCTGCCAAGACAAAGATATATTTTGCTACTGCTGTTGCTTTGTGGGATGCAGAGTTCTACATTAAAGTTGATG

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|193442857|gb|FK404235.1|FK404235
EST:     ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTG                         GATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
genomic: ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTGgtaatgatcc ... gatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
EST: gi|193461810|gb|FK426351.1|FK426351
EST:     ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTG                         GATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
genomic: ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTGgtaatgatcc ... gatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
EST: gi|20498515|gb|BQ273445.1|BQ273445
EST:     ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTG                         GATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
genomic: ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTGgtaatgatcc ... gatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
EST: gi|193377662|gb|FK343202.1|FK343202
EST:     ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTG                         GATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT
genomic: ACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTGgtaatgatcc ... gatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaataaaaaaaaagaaatgcaacaagtttcaaacctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG
                                         ttttgat  putative branch site (score: 4)
                                               tttttc  CT-rich tract
     taaaaaaaaagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatcctctttgtcttattgctgttttccccgttgtctcttctatcatttgtctctacttgaataatcacttgataagatatcatggtcacatttatttgaaggaaaaattaaataaaaaaaaagaaatgcaacaagtttcaaacctctgttttgatttttcagGATCATGTTGAAGGATACCTTGAATTGTCAGCAAAGACAAAGACATACTTTGCCACTGCTGTTAACTTATGGGATGCTGACTTCTATATCAAAGTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG