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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG

Basic information

species Glycine max
transcript GLYMA19G33700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtctcacatattcattctcattccacctttt--cctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
                                    || ||   |     |     ||||   |  |   |  | || | |   ||||    |      || ||   |  | |  |     | |         |   ||||||||||||||||||||||||||| || ||  | |||||||||||||||||||| || || ||||| ||||| || |
gtgaggctccggttcttctccacttcgttctgtcccgtttcgtttccctgtgtgtcttccctttgctgatccgtatggtgcaaattttcccccgcgaatttttttggtgcggatttggggcgtggggggtttcgctgcagGTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 1
-----------gtctcacatattcattctcattccaccttttcctttttgttactctttttttttctt--cttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
            || | | |     | | | | |||  |||   ||||| |  |  |||||| |  ||  ||  ||| |  |      | |      || | ||  | |   ||||||  ||||||||||||||||||| || ||| | ||||||||||||||||||||    || || |||||||| || |
gtaatccgcggctcccgcttcgctctccccttcccagatttgtttttttttctcctttttttgtggttaactggttcgtttcccgtgcgatttctcccgccgaattcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGGCACCACCGTCCATGGCACCATCACTG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 1
----------gtctcacatattcattctcattccacctt--ttcctttttgt-tactctttttttttcttc--ttcttcttcactttgaagctaaa--aagcgtctaaa----actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
           || | | | ||  | | | |||| |||   ||| |||  || | ||  ||  |||  | |  || |    |   | |  ||  |     |||    ||     ||   |||||||  |||||||||||||||||||||| ||  | |||||||| ||||||||||| || || ||||| |||||||| |
gtaagccagcatccccc-tgtttctcccctttccccctccattcgtttcagtctgctgattcgtttggtgcaattttcgcccgaatcggtgcggattttggcgcgggaattgcgcttttacagGTTCTTGATGAAGCTGAACAACGAAACGGTGACCATCGAGCTTAAGAACGGCACCGTCGTACACGGAACCATTACCG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027571_T02 (Zea mays), 3'ss of exon 1
------gtctcacatattcatt--ctcatt-------ccaccttttcctttttgttactctttttttttcttctt-----cttc-ttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
        | | | ||||| ||  | ||||           |||  | ||   ||| |||     |    ||  |     ||||    | ||||  ||| |     ||      | |   |||||| || |||||||||||||| || || ||  | |||||||||||||||||||| ||||| ||||||||||| || |
gtaacgcccccccgtattcgttcgcccattgttagggttggcttccctttaccgttcctcgccgctccgtttgctacgaacttcgcctattttggtgctcatttcggtgcgcttc-gccgcagGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
---------------------gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtct---aaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
                        | |  | |||  | | |||  |   ||| |||     |  |    ||| |  || || |  | | ||| || | |  |   ||| |    |   |    ||||||| |||||||  ||||||||||||| || ||||||||||| |||||||| ||  ||||||| || |||||||| |
gtatggtttctactcggattctctttatttcttcggtttaattgga--atttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtctcacatattcattctcattccaccttttcctttttgttactctttttttttc-ttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
                     ||  | | ||  |||  |||  ||| || ||||| ||||  ||    | | |  | |||    |   | |||  |    ||||||| |||||||||| |||||||| || || ||||| |||||||||||||| || |||||||| |||||||| ||||
--------------------gtctgcttatt--tttcagtttttctcttgttttcattctcattaactattgttgacctagcttgatacgaaattt----cagGTTTTTGATGAAGCTCAACAACGAGACTGTGTCAATTGAGCTCAAGAACGGTACCGTTGTTCATGGCACCATCACAG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
          || ||  ||| |  |        |   | |     | |   ||| ||  | || ||   ||  |  || | ||   | ||      ||||||||||||||||||| |||||||||||||||| || |||||||||||||| || || || ||||| |||||||| ||||
--------gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttataa---tttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ29766 (Selaginella moellendorffii), 3'ss of exon 1
gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
    |       |||   |||  |    | |||| ||| |    |      |||    ||||    ||||   |  || |      |       |    ||| |||||||||||||| |||||||| || ||||| |||||||||||||| || ||  ||||  | || || || ||||
-gtacgtcggcgcatctccatcgc---ctctcctctttctcttccacagggtttagggttctcgcgcactgacagtctgat-----ttctcgcttctcccagATTTCTGATGAAGCTAAACAACGAGACAGTATCCATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAG

upper sequence: GLYMA19G33700.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ08912 (Selaginella moellendorffii), 3'ss of exon 1
gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
||    ||    |||   |||  |    | |||| ||| |    |      |||    ||||    ||||   |  || |      |       |    ||| |||||||||||||| |||||||| || ||||| |||||||||||||| || ||  ||||  | || || || ||||
gtacgtca-gcgcatctccatcgc---ctctcctctttctcttccacagggtttagggttctcgcgcactgacagtctgat-----ttctcgcttctcccagATTTCTGATGAAGCTAAACAACGAGACGGTATCGATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAG

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|208046916|gb|GD846477.1|GD846477
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|13789125|gb|BG651716.1|BG651716
EST:     AAAACCCTGCC-TCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|12691282|gb|BG157618.1|BG157618
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|298184695|gb|HO029908.1|HO029908
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|6913873|gb|AW395403.1|AW395403
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|58014996|gb|CX701738.1|CX701738
EST:     GTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: GTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|14126660|gb|BG791098.1|BG791098
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|9902628|gb|BE611526.1|BE611526
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|298163152|gb|HO011885.1|HO011885
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|18848707|gb|BM567819.1|BM567819
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|19268677|gb|BM884933.1|BM884933
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|14126440|gb|BG790878.1|BG790878
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
EST: gi|192311957|gb|FK004560.1|FK004560
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAG                         GTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTCGTCAGgtctcacata ... actgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG
                                      gtctaaa  putative branch site (score: 3)
                              taaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcacatattcattctcattccaccttttcctttttgttactctttttttttcttcttcttcttcactttgaagctaaaaagcgtctaaaactgaaacagGTTTCTGATGAAGCTGAACAACGAAACCGTATCAATCGAGCTCAAGAACGGCACAGTTGTTCACGGCACCATTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC