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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG

Basic information

species Glycine max
transcript GLYMA14G17930.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
--------gttttgttgctgtgatt-ttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
        || |   ||  |   |  | |||| ||  ||   ||| | | |  | |||| |         ||  ||     || ||  |    | | |  | | |||||||| ||||||||  | | |||||| |||| ||| ||||||||||||||||||||||| || ||| | ||||| || ||||| || ||||
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatct--------gattcttccactttcaactga-gttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 2
gttttgttgctgtgattttattttttgttttgttctactattaggtt---tattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
 | ||  ||     || |  |  |     |||| |||  | |   ||     ||  |   |    || |  |||  ||     ||  ||| || |   |||||||| |||||||| |||| ||||||||||| ||| ||||| || |||||||||   || || ||  |||||||  ||||||| || ||||
-tattcctgactcaatatagtggtaccccttgtactataagttatttggacgttgcgggtatgtttgttgatgtaattttcaagtg-tatttt-tccatgcagTGTCTGGGTTGCCCGTAAACCACCTGGTTTTGCATTTATCGATTTTGATGACAAGAGGGATGCTGAGGATGCACTCCGTGATTTAGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027105_T02 (Zea mays), 3'ss of exon 2
-----gttttgttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG-----------
       | | |||   | | |    | |   |||| || ||| ||   | ||||| | |    | ||| |||    |  | ||  |  | |  | |   |||||||| ||||||||  | | |||||| || | ||| || |||||||||||||||||||| || ||||| ||||| || |||||||||||||           
caagaaatgtattgaactcaataccatatcactttttttgtacaat--agattattat-agtttatatgctttcacttggactgatt--tgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATGGTACTTAATAA

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G070239_T02 (Zea mays), 3'ss of exon 2
-gttttgttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
      | ||  | | |||||| | || | ||  | ||| | |   ||  || | | |  ||    |  ||   |  |       | |||| |   |||||||||||||| ||||| | ||||||||||| ||| |||||||| ||||| ||| | || || ||| |||||||||| |||||  | ||||
tagcgagatggagaggttttatctgttatatttctttacgacttctttcgttatcagatgaacacctggtgcagtccactaactgt-tgttctcaatgcagTGTTTGGGTCGCACGCAAACCACCTGGTTTTGCATTTATTGATTTTGACGACAGGAGGGATGCAGAGGATGCTATTCGTGATCTAGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G070239_T04 (Zea mays), 3'ss of exon 2
gttttgttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
               |||||| | || | ||  | ||| | |   ||  || | | |  ||    |  ||   |  |       | |||| |   |||||||||||||| ||||| | ||||||||||| ||| |||||||| ||||| ||| | || || ||| |||||||||| |||||  | ||||
--------------gttttatctgttatatttctttacgacttctttcgttatcagatgaacacctggtgcagtccactaactgt-tgttctcaatgcagTGTTTGGGTCGCACGCAAACCACCTGGTTTTGCATTTATTGATTTTGACGACAGGAGGGATGCAGAGGATGCTATTCGTGATCTAGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027105_T06 (Zea mays), 3'ss of exon 1
-----gttttgttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
       | | |||   | | |    | |   |||| || ||| ||   | ||||| | |    | ||| |||    |  | ||  |  | |  | |   |||||||| ||||||||  | | |||||| || | ||| || |||||||||||||||||||| || ||||| ||||| || |||||||||||||
caagaaatgtattgaactcaataccatatcactttttttgtacaat--agattattat-agtttatatgctttcacttggactgatt--tgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 2
---gttttg-ttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactat-gttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
   |||||  ||| || |   ||    ||| |||| |  |  | | || |  | ||||        | |  | |||      |   ||| | ||| |   |||||||||||| ||||||||| ||||||||| | ||| |||||||| ||||| ||| | || || ||  |||||||||| |||||  | ||||
taggttttacttgttgcgtcctttgcgttttttttttctt--tgtgagatggagtttgttgtt---tcacctggtgcaggtcgctaactgttgttctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: AT4G31580.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttgttgctgt-gattttattttttgttttgttctactattaggtttattttgaaa--aaaaatg----attttgtgtttaatgggtact-atgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
     ||     |  ||   ||   |   || |  |||| |||  ||   |||||||   |||| |     ||||||  | |      |  | || |    | ||||||||||||||||| ||||||||||||||||| |||||| | || || || || |  || || || |  |||||||||||||  || ||||
-----gtaagaatcaatccaatcaatcagttcgcgctacaattttgtcacttttgaagttaaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG

upper sequence: GLYMA14G17930.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
gttttgttgctgtgattttattttttgttttg--ttctactattaggtttattttgaaaaaaaatg--attttgtgtttaatgggtact-----atgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
          |  | |||| |||   |||| |  |   || |||  ||  ||| || |   || |   ||||     ||  |   |  |     ||||| | | |||||||| ||||||||||| |||||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| || |||||||| ||||
---------ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG

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|298170870|gb|HO015846.1|HO015846
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|213589771|gb|DB969592.1|DB969592
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|13790205|gb|BG652796.1|BG652796
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCTTTGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298179401|gb|HO027872.1|HO027872
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|16996626|gb|BM085998.1|BM085998
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298185492|gb|HO030705.1|HO030705
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|7285723|gb|AW598210.1|AW598210
EST:     AGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: AGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|207702915|gb|GD686149.1|GD686149
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|192299813|gb|FG993333.1|FG993333
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACTTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|8669525|gb|BE190632.1|BE190632
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|209700148|gb|BW652992.1|BW652992
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298198145|gb|HO039684.1|HO039684
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298164978|gb|HO011027.1|HO011027
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|6070422|gb|AW099809.1|AW099809
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTGTGGGTTGCACGTACACCACCTGGTTATGCTTTTATTGACTTTGATG
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTT-TGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATG
EST: gi|298178379|gb|HO024114.1|HO024114
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|7591104|gb|AW706844.1|AW706844
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298179203|gb|HO027674.1|HO027674
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGATTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298165150|gb|HO011199.1|HO011199
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCCTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG
                          gtttaat  putative branch site (score: 4)
     tttgaaaaaaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgttgctgtgattttattttttgttttgttctactattaggtttattttgaaaaaaaatgattttgtgtttaatgggtactatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGACGCACAGGATGCTATCCGTGAATTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG