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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA

Basic information

species Glycine max
transcript GLYMA02G46380.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 12
---gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
      | |||||  ||||  ||| |      | ||  || ||        |||  ||| | || || |          ||   |||||  |||  |||||  ||||||| || ||||  |||||||||||||| |||||||||||||| || |||||||| |||||||| ||||| || ||||| || || 
gtacgctctctctccacatgcattggcacacctgtgtgtggataaggacttttagttct-gacactcgt----------tttctttgca--gCATGTCTGTTGTTGAGGAAAGCTTTGAATATCTTGATGCACCAGTTGAGAGAATTGCTGGAGCTGATGTACCCATGCCCTATGCTGCCAATCTTGAGAGG

upper sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 3'ss of exon 10
gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
||  |||||| |   |   | |   | |   |     |  ||  |||  | ||   | |   ||||  ||   |   |||  |   |||||  |||||  | ||||| || ||||  ||||||||||| || |||||||| ||||| || |||||||| |||||||| || || || || || || || 
gtccatctctctctctctctctcgctctccctctccctcgctctctg--tgacaagttgttctcatatgtac-tgtatcttctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGG

upper sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G043198_T02 (Zea mays), 3'ss of exon 11
gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
||    | || | | |   |   |  ||       | ||   ||  |  |   |||      | ||| || || | |   | |   |||||  |||||  | ||||| || ||||  |||||||||||||| || ||||| ||||| || |||||||| |||||||| || || || || || || || 
gtcggccactctccctccctccctccttcccaatgtataatgtatagtctgcgtctc--tcgtaatgggt-tgaaatgtgcctttgcagCATGTCTGTTGTAGAGGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGG

upper sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 12
gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactct-tggcaatcatgagtgtg-tacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
                      ||| |     |    || | |       |  | | ||| |   || | | |   || | | |    |||||  |||||  | || || || || |  || ||||||||||| |||||||| ||||| || |||||||| || ||||| ||||| || || || || |||
----------------------gttctctctagcccttaccctctcacacatttgtgtggtatctattattctaacacatgtttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGA

upper sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 13
gtttatctctttacattgatttgtttttg-tatgaatgtatctt--actggttaactcttggcaatcatgagtgtgtacttctcttgca------cagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
||| |  ||  | | || |||   |   | | | | | |  | |  | ||  |||   ||   || || |  | |  |||| |   | |      |||  | || ||  | || ||||| |||   ||  | ||||||||||| ||||| ||||| || ||||||||||| ||||| |||||||| || || || |||
gttaacttcaattccttaattcaatagagatcttattatcacctggattgtataatagttttaaaacacggat-taaactttttccgtaatggatcagTGCGTCGGTTGTAGAAGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGA

upper sequence: GLYMA02G46380.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 12
------gtttatctctttacattgatttgtttttgtatgaatgt-atcttactggttaa-----ctcttggcaatcatg--------agtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
       | | | ||   | ||  ||  |  |  |   |  ||| ||  |  ||||| |     ||| |   ||  ||         |  |||| ||    ||   ||| |  ||||| ||||||||||| |||| || |||||||||||| || || || ||||| ||||| ||| |||||||||| |||||||||||||| || |||
gttaccttctttttcaccaaatctatg-gcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgt-ctgaatttctgcagTATGTCTGTTATTGAGGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGA

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|209708510|gb|BW668120.1|BW668120
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
EST: gi|7028855|gb|AW458638.1|AW458638
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
EST: gi|6846711|gb|AW349001.1|AW349001
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
EST: gi|208141778|gb|GD939550.1|GD939550
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
EST: gi|11273897|gb|BF324286.1|BF324286
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
EST: gi|21887778|gb|BQ740991.1|BQ740991
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGANGAGAGTTTTGGTTATCTTGATGCA
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCA
EST: gi|22926912|gb|BU544051.1|BU544051
EST:     GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTNGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: GTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
EST: gi|6454269|gb|AW184952.1|AW184952
EST:     AGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTG                         CACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG
genomic: AGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctct ... tcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA
            ggttaac  putative branch site (score: 3)
                                       tacttctctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatctctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacagCACATCTGTCATTGAGGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT