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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 1
gtacaatc-tttttgttttttcttctgcttctgtaacccta-accctaatcctatcga---ttacactatcttttttgctgcttccgtcttcttagccattagggtttctgatt--tttaattgaattg------tttttggtggc---------tgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
| |    |   |  | | | |||    || |  |||||||| | ||   |||   |||   ||   | |  |   |       |   ||||       ||||||||||| |  |  | | || |  |||      |||||||||            | |||| ||| ||||| ||||||| |||||| ||||||||| |||||| ||||| |||||||| |||||||||||||||||||| |||||| | ||||||||||
gcaagcccgcctccgctctctctctctctcccctaaccctagatccccctccctccgaggtttttgccagttgcctcctccggtgaatctttgcttggattagggtttccgggtcgtctgatcggtttggggttttttttggtgtgattttggtgcgcagGATGAGCTGCAGCGGACCAACTTGGAGCTGGAATCGTTCAAGGAGAAGATTAAGGAGAACCAGGAGAAGATTAAGCTCAACAAGCAGCTTCCCTACCTCG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 1
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgttt--ttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                      | |||| || |  | ||  | |     |    |   || ||| |||||   |        || ||   |  ||| ||   |||||||| |    |  |||| |  | ||  ||   |||| ||| ||||| |||| ||  | ||| ||||||| |||||||| |||||||||||||| ||||||||||| || ||||| |||||| |||| ||||| |
---------------------gtttgct-ctctctctctctctccgcctccgcgggaaaccctagcttttgccccagcgatctcctccatgggatttgg---tctgatttgtggg-ggtttgtctcatcgggtgcctcagGATGAGCTGCAGCGGACGAACCTTGAGGTGGAATCCTACAAGGAGAAGATCAAGGAGAACCAGGAGAAGATCAAACTCAACAAGCAGCTGCCTTACCTTG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G032505_T01 (Zea mays), 3'ss of exon 1
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagcca-ttagggtttctgatttttaattgaattgtttttggtggc-tgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                               || | |   | || | |||||      |  |   |   || |   |||| |  ||         ||  | | | ||   |||  |||  || | | | |  ||    |||| ||||||||| |||| ||  |||||||||| |||| |||||| ||||| ||||| || || ||||| ||||||||||| |||||| ||||||||||||
-------------------------------gtgagc--gagcccagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttctgatctgtggggtttgtttggtttttctcttgccgcacccagGACGAGTTGCAGCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAAGAGAAAATTAAGCTCAACAAGCAGCTGCCCTACCTCG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 1
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagcca-ttagggtttctgatttttaattgaattgtttttggtggc-tgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG------------
                               || | |   | || | |||||      |  |   |   || |   |||| |  ||         ||  | | | ||   |||  |||  || | | | |  ||    |||| ||||||||| |||| ||  |||||||||| |||| |||||| ||||| ||||| || || ||||| ||||||||||| |||||| ||||||||||||            
-------------------------------gtgagc--gagcccagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttctgatctgtggggtttgtttggtttttctcttgccgcacccaggacgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAAGAGAAAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 1
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                           | | | ||||||| |||||  ||    |    |     |     ||  |   | ||  ||| |   ||| ||| |     ||||    ||          ||||     |||| ||| ||||| || | ||  ||||| |||| ||   |||||| |||| ||||||||| |||||||||||||||||||| |||||| |||| |||||||
--------------------------gtgcggaaaccctagccctagccccgctg--cgcgtcgcccagagtgtcgggactgt--tctgattgatttgggat----gttttgggctg----------ggtgttcatagGACGAGCTGCAGCGGTCGAACCTGGAGCTGGAGTCTATCAAGGAGAAGACCAAGGAGAACCAGGAGAAGATTAAGCTCAACAAGCAGCTGCCGTACCTCG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                                 |||  | |   | ||   || ||  |  ||| | | |||  || | |    |   ||    ||    || || || ||   ||   || |||   | || |  |||||||   ||| || || ||| | || |  || || |||||||| ||||| ||||||||||||||||||||||| ||||| |||||| |||| ||| | |
------------------------------ctcaac--tgagattgattgaattgaaaa-gcta-cgtctttcttgttgcaaattggata--tgttgaaattgctcatcttgtgttt--ttctttgatggggatttagGAAGACGCGCAAAGAACAAATCTAGAATGTGATTCTTACAAGGAGAAGATTAAGGAGAATCAGGAGAAGATTAAACTCAACAAGCAGCTGCCTTACTTGG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 1
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                                          |   || || ||  ||   |  ||||| |   ||  ||  ||         ||| | | || ||||   |  | |   || | | ||||  ||||||| |||||||||||||| ||  |||||| ||| || || ||||| |||||||||||||||||||||||||| |||||||| |||||| | |||||| | |
----------------------------------------gtctctattctctctctttttc--tctttatatatgtgtctttccgtgatatgatttgcgattttgatgaatggtggtggtggtat-ggtg-ttgaagGAGGAGTTGCAGAGGACGAACATGGAGTGGGACTCCTATAAGGAGAAGATCAAGGAGAATCAGGAGAAGATCAAGCTCAACAAGCAGCTTCCCTACTTGG

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 1
---------gtacaatctttttgttttttcttctgcttctgtaacccta-accctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
         |  |  |   | ||      ||  | | |   |     |  |   || ||  |    || |        | | |  || |  |  |   | |   |  |  ||    ||  |    ||  | |  || | |  |   |||| ||   ||| ||        ||||    ||  |    || || || |||||||||||||| |||||||| ||||| ||||||||| |||| ||||| |
gttttttctgcgccttgagtatggcgcgcctggttcatggttggatatgtatgttagtctgaggtcttgctgggggggtgtagtagcatggggttgtgtcgaggtgtgaattatcaatgatcggatgggtgggattggatttc---agGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATCAAGGAGAATCAAGAGAAGATCAAGCTGAATAAGCAGCTGCCTTACCTTG

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|6482551|gb|AW201806.1|AW201806
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|6915777|gb|AW397307.1|AW397307
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|298171738|gb|HO021330.1|HO021330
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|193703110|gb|FK639626.1|FK639626
EST:     GTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: GTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|298167852|gb|HO013115.1|HO013115
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGGGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|4313874|gb|AI460993.1|AI460993
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|33390542|gb|CA853737.1|CA853737
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|298195561|gb|HO043952.1|HO043952
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|209719376|gb|BW674456.1|BW674456
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|7924448|gb|AW830474.1|AW830474
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|27427306|gb|CA938826.1|CA938826
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|18040691|gb|BM308985.1|BM308985
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|213598762|gb|DB968233.1|DB968233
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
EST: gi|7042249|gb|AW472143.1|AW472143
EST:     ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAA                         GAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC
genomic: ACGTCGTCAGAGCTTCTCGTCTTCTCGACAACGAGATTCGCATCCTCAAAgtacaatctt ... gtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG
                         ttttaat  putative branch site (score: 3)
                 tttctgatttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatctttttgttttttcttctgcttctgtaaccctaaccctaatcctatcgattacactatcttttttgctgcttccgtcttcttagccattagggtttctgatttttaattgaattgtttttggtggctgaagGAAGAGTTGCAGAGGACCAATTTGGAGTTGGAATCGTACAAGGACAAGATCAAGGAGAATCAGGAGAAGATTAAGCTCAATAAGCAGTTGCCCTACCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA