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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT

Basic information

species Glycine max
transcript GLYMA11G05190.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
                   |    || |  ||||   |        ||  |  | |  ||     |  ||||| ||     |||| | ||   | |  | ||  |||          |       |||| | ||| || || || ||||| |||||  | ||||| |||||||| ||||||||||| |||||||| ||  | || |||||||||||||| |||||  |
-------------------taaactaacataaaat--ttattaatgtggaaaatcaagaatttcctagtttgt-ttcataacttactcttgactgttctttgtacttctgcttggcatt------cagGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
                                     ||  || |   | |  |  | ||| |  | | | |   |   | |||  |  |  |   ||  || |  | | ||    || |   |||||| |  || ||||| ||||| || || ||  |||||||||||||||| |||||||| |||||||| || || || || || || ||||| || || ||  |
------------------------------------gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgct--tgatctgctgctgctgctgcttgtg--ttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
                      ||      |  |  |   ||      |    |   ||| | |   |||||  ||   |  ||   |  ||   |||||||||         ||      ||| |||||| ||| ||  | || ||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||| | ||||| || || ||||| || ||  |
----------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaat-cattttggattccttgtttgacac-agc--tcttatgat---------aa------tcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgt--tttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
                        ||    |||  |||   |||  |      ||||  ||| | |  ||||| |    |  | || |  |   || | |  | |  ||   | | |  |   |   |||||| ||| || || || |||||||||||  | ||||| |||||||| ||||||||||| ||||| |||||||| ||||| |||||||| ||  | ||  |
-----------------------gtaagttaaagaaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4
gttagaaagtt--aatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
|| ||||      |  ||  || |   |   |||   | |  | | | ||    || | | |||||  || || | || ||     ||| ||  |  || | |  | || ||  ||        ||  ||||| ||| |||||||| |||||||| ||  ||||||| |||||||| ||||| ||||||||||| |||||  | || || || || || | |||||| ||
gtaagaagaccccatcttgcttcttccatttcaa---agttacttccttgttttgtcaaataaacttcttctt-ttttctccctacattttttttattccttttttttttcaaaca--------cttaagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 5
gttagaaagtt--aatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
|| ||||      |  ||  || |   |   |||   | |  | | | ||    || | | |||||  || || | || ||     ||| ||  |  || | |  | || ||  ||        || |||||| ||| |||||||| |||||||| ||  ||||||| |||||||| ||||| ||||||||||| |||||  | || ||||| || || | |||||| ||
gtaagaagaccccatcttgcttcttccatttcaa---agttacttccttgttttgtcaaataaacttcttctt-ttttctccctacattttttttattccttttttttttcaaaca--------cttcagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACTGAGCCACCTACTGATGACTT

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 7
----------gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttc--ttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
            ||    | |  |    |||| | |    ||    | || |    |       |  |  | ||  |||  | | |  |  |  || ||  | || ||||||    |||  | |  |  | |    ||||| ||||| || || || || ||||| ||||||||||| ||| |||| |||||||| || || ||||||||| | |||||||| ||||| || || ||  |
gtaaattttcagtattgcgcttctcggtttttttgaattaaaggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacg--acgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT

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|6073022|gb|AW102409.1|AW102409
EST:     ATTTCACATCAGCCTGCTTAACAG                         GAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
genomic: ATTTCACATCAGCCTGCTTAACAGgttagaaagt ... ctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
EST: gi|18733946|gb|BM527900.1|BM527900
EST:     -GTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTGACAG                         GAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
genomic: TGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTAACAGgttagaaagt ... ctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
EST: gi|17519533|gb|BM188575.1|BM188575
EST:     TGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTAACAG                         GAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
genomic: TGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTAACAGgttagaaagt ... ctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
EST: gi|14008637|gb|BG725241.1|BG725241
EST:     CGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTAACAG                         GAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
genomic: TGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTAACAGgttagaaagt ... ctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
                             atcttac  putative branch site (score: 3)
                                       caatttctctctcc  putative PPT
      ttcttattattagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA