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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttgatgaggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG

Basic information

species Glycine max
transcript GLYMA08G45270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 2
-----tacttgatgaggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatg--cagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG
     | ||   |  | |   |  ||||  ||   | |  ||     | | ||    |          |||| |  | |    ||| || || | |    ||   |||||||||||| || |||||||| || ||||| || |||||||||||||| || ||||| || || ||||| || ||||||||| |||| | |
gtgagttctgcttttgctttcatttttgattaatatatggtcgtggataaaaaaagcttg-----acgaatggtcttgattgatatgttgtgacttgaattggttagGTGTTGCTGGAGGCGCAGCATCGGGAAAGACTACTGTTTGTGATATGATAATCCAGCAACTGCACGATCAGCGTGTTGTACTTATTAACCTG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 2
tacttgatgaggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG
           ||   |    |||     | | ||| | || |  |||   |  ||  |     |  ||  |||     |  | ||||       | |||| |||||||| ||||||||||| || || ||||| || |||||||||||||| ||||| || ||||||||  ||| |||  |||| ||||||
-----------gtgagagtcgtgg-----tggattttagtt-taccaaagatggttagaaacagaaaatgttaaatagaaaatgttgtt------ttcagGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACTGTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 2
tacttgatgaggtcctaaat-ttggataccttgttttcaattcttacaacttttcttttatctta-atgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG
    |  | || | ||   | || |  ||  | |||   ||| ||  ||||  |  ||||    |  ||  | | |  || ||      | |||||    ||||||||||||||||||||| ||||| || || ||||||||||| ||||||||| ||||||| |||||||| || |||||||| || || |||
-gtgttgttagatgcttgttgtttggcactctttttatcatttttttaactcatagtttaaaacacgtgtatgtgattct-atcaaacattatatgggctagGTGTTGCTGGGGGTGCAGCTTCTGGGAAAACTACAGTTTGTGACATGATTATTGAGCAGCTGCATGATCAGCGTGTTGTACTAGTAAACCAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------tacttgatgaggtcctaaatt----tggataccttgttttcaattcttacaact-----tttcttttat---cttaatgattctaacact-------tattttttgtcatatga---------tgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG
                                                     |  |||   |   | | ||||    ||| |   |||  |     |  |   |||     |||  || |    || |||||   || |  |            |  | ||||||          ||||||||| || || ||| | || || || |||||||| || ||||| ||||||||||| ||| | || ||||| || ||||| ||||||||||||
gttagtgaagaggacttgctcactcgtgcgctcgcctcgtcgtcgtctgtttatttttgtcaaaaacattaattcgtttggtttttttgcctatgcctgctttgactgaaaatttgcttaacgtgctaaatgaagttagctttgtacgtgcggcctaagacatatgggtttgtgcgtgcagGTGTAGCGGGAGGTACTGCGTCGGGGAAGACAACTGTGTGTGACATGATTATTCAACAGTTACACGATCACCGTGTTGTGCTTGTTAATCAG

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S83_234V6.1 (Physcomitrella patens), 3'ss of exon 3
-tacttgatg-aggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG--------
 ||| |  || ||||    |   | |  |  ||||      | |  |  || | |   |  |   ||| | || ||   |||  ||||    | |||  |||| || ||||||||| | |||||||| ||||| || || ||||||||||| |||||||||||||||||||| || ||||| || || || ||         
gtacgttgtgtaggtgtccagcattgtgagattgt----ggtgcgaattacgtcttggtagtgggaattactcaaatttttagctttt----tctga-acagGAGTGGCTGGGGGTACTGCATCTGGAAAGACCACCGTGTGTGATATGATCATTCAGCAGCTTCATGATCATCGTGTTGTCCTCGTCAACCAAGACTCGTT

upper sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S370_24V6.1 (Physcomitrella patens), 3'ss of exon 1
-tacttgatgaggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG--------
 ||| |   || ||     | | |   |   || |||     |  | ||||| ||    ||   |||     |    |  | || |||   | |   ||||| || ||||| ||  | |||||||| |||||||| || ||| ||||||| ||||| |||||||||||||| || || || ||||| || ||         
gtacgtttcgatgtagctcactggtgaa---tggttttggggcgaaaaacttatcaagaatgagaat-----tggtcccaacttgttgctttcttgagcagGAGTGGCTGGAGGCACTGCATCTGGGAAGACAACTGTATGTAATATGATCATTCAACAGCTTCATGATCATCGTGTAGTTCTTGTAAACCAAGACTCGTT

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|209716820|gb|BW654339.1|BW654339
EST:     ACAACCAACAACCTCAGAAACTGACATGCATAAACAACCTTTTGTCATAG                         GTGTTGCTGGGGGTGCAGCATCTGGCAATACAACAGTTTTGTGATATGATT
genomic: ACAACCAACAACCTCAGAAACTGACATGTATAAACAACCTTTTGTCATAGgtgtgctttc ... tatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTT-GTGATATGATT
EST: gi|13478669|gb|BG508053.1|BG508053
EST:     AACCAACAACCTCAGAAACTGACATGTATAAACAACCTTTTGTCATAG                         GTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTA
genomic: AACCAACAACCTCAGAAACTGACATGTATAAACAACCTTTTGTCATAGgtgtgctttc ... tatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTA
EST: gi|15200732|gb|BI424501.1|BI424501
EST:     ACAACCAACAACCTCAGAAACTGACATGTATAAACAACCTTTTGTCATAC                         GTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTA
genomic: ACAACCAACAACCTCAGAAACTGACATGTATAAACAACCTTTTGTCATAGgtgtgctttc ... tatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG
                       ttctaac  putative branch site (score: 1)
     tttcttttatcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttgatgaggtcctaaatttggataccttgttttcaattcttacaacttttcttttatcttaatgattctaacacttattttttgtcatatgatgcagGTGTTGCTGGGGGTGCAGCATCTGGCAAGACAACAGTTTGTGATATGATTATTCAGCAGCTTCATGATCAACGAGTTGTACTTGTTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- cttgatg
- - - - - - - - - - - - -taccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaacac