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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgccattctgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaacttgtttcttattgtagtagtttttttccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG

Basic information

species Glycine max
transcript GLYMA19G27250.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27250.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067476_T01 (Zea mays), 3'ss of exon 3
ccatgccattctgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaactt---gtttcttattgtagtagt-ttttttccctatt--agGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG
     ||    ||        || |  |  |    |||||| |    |   || |  ||  ||||     || | |   |  |  | |  ||| | | | ||  |||||||||| ||||||||||| || ||  ||||| ||||  |||| |||||||| ||||||||||||||||||
----tccgacttgaaaacattgctactgtac-ataatttagtagtgttt-cttgtattgtccaacccacggtgtttcgctaaatcaatgctttgtacatgttgaagGAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGG

upper sequence: GLYMA19G27250.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067476_T02 (Zea mays), 3'ss of exon 3
ccatgccattctgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaactt---gtttcttattgtagtagt-ttttttccctatt--agGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG----
     ||    ||        || |  |  |    |||||| |    |   || |  ||  ||||     || | |   |  |  | |  ||| | | | ||  |||||||||| ||||||||||| || ||  ||||| ||||  |||| |||||||| ||||||||||||||||||    
----tccgacttgaaaacattgctactgtac-ataatttagtagtgttt-cttgtattgtccaacccacggtgtttcgctaaatcaatgctttgtacatgttgaagGAGGCATACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACCTCCAGAGAAGAAGTTTGAATGGGTAA

upper sequence: GLYMA19G27250.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 3
---------------------------------------------------ccatgccattc-tgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaacttgtttcttattgtagtagtttttttccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG
                                                     |||  || | |   |||  | ||     |||    |||  || | ||  |  ||||         | |   | | | || |  ||| | ||  |   ||||||| || ||||||||||| || ||  ||||| ||||  |||| |||| ||| ||||||||||||||||||
gtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcc-----tcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaagGAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGG

upper sequence: GLYMA19G27250.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G376727_T03 (Zea mays), 3'ss of exon 3
---------------------------------------------------ccatgccattc-tgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaacttgtttcttattgtagtagtttttttccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG----
                                                     |||  || | |   |||  | ||     |||    |||  || | ||  |  ||||         | |   | | | || |  ||| | ||  |   ||||||| || ||||||||||| || ||  ||||| ||||  |||| |||| ||| ||||||||||||||||||    
gtcccccccccccccccccccgacctctactatacataattttagtgtttcttatgttatacatcttgtattatcc-----tcttattttttacatcgctattgcttggcccatggtatttagttaaatctaatgttttgtatctgttcaagGAGGCCTACTCAACTCCCATCTTCCCACTGGATATTCTCGCTGAGAGACTTCCTGAGAAGAAGTTTGAATGGGTAA

upper sequence: GLYMA19G27250.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g01370.t01 (Vitis vinifera), 3'ss of exon 3
ccatgccattctgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaacttgtttcttattgtagtagtttttttccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG
                     | |||   |     ||         ||  |||   ||||  || || |    | |||    | ||||      | ||||||||||||||||||||| ||||| ||||| ||| | ||| | |  |||||||| |||||||||||||| |||
-----------------gtttgacattttttatttatgatttgtttctcgtttcatgtgaagaatttctaatctcttg----acttttgcctgtttttagGAGGCATATTCAACTCCAATATTACCTTTAGATATCCTTGCAGTGAGACCTCCAGAGAAGAAGTTTGAGTGG

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|6913960|gb|AW395490.1|AW395490
EST:     GTGAACCAGCTGTCATAAAGTTCCGTGTTCCCACAAAGGCTGCTTTGCAG                         GAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCT
genomic: GTGAACCAGCTGTCATAAAGTTCCGTGTTCCCACAAAGGCTGCTTTGCAGgttaatatct ... tccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCT
EST: gi|15815757|gb|BI788032.1|BI788032
EST:     TGAACCAGCTGCCATAAAGTTCCGTGTTCCCAACAACG-CTGCTTTGCAG                         GAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGA
genomic: TGAACCAGCTGTCATAAAGTTCCGTGTTCCCA-CAAAGGCTGCTTTGCAGgttaatatct ... tccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGA
EST: gi|23064074|gb|BU578847.1|BU578847
EST:     GTGAACCAGCTGTCATAAAGTTCCGTGTTCCCACAAAGGCTGCTTTGCAG                         GAGGCATATTCAACTCCCATATTGCCTTTGGATNGT-CTTTCTGATAGACC
genomic: GTGAACCAGCTGTCATAAAGTTCCGTGTTCCCACAAAGGCTGCTTTGCAGgttaatatct ... tccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGAT-GTTCTTTCTGATAGACC
EST: gi|13791278|gb|BG653869.1|BG653869
EST:     GTGAACCAGCTGTCATAAAGTTCCGTGTTCCCACAAAGGCTGCTTTGCAG                         GAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCT
genomic: GTGAACCAGCTGTCATAAAGTTCCGTGTTCCCACAAAGGCTGCTTTGCAGgttaatatct ... tccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgatttttggtgagcaacttgtttcttattgtagtagtttttttccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG
 cactgat  putative branch site (score: 3)
                                       tttttttccctatt  putative PPT
                                    tagttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgccattctgccgtagcagccatggctctgccatttagcaacactgatttttggtgagcaacttgtttcttattgtagtagtttttttccctattagGAGGCATATTCAACTCCCATATTGCCTTTGGATGTTCTTTCTGATAGACCTCCCGAGAAGAAGTTTGAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-catgcca
- - - - ttctgcc
- - - - - - - - - - agccatg
- - - - - - - - - - - - - - ctctgcc
- - - - - - - - - - - - - - - - - - - - gcaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - tttggtg