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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG

Basic information

species Glycine max
transcript GLYMA10G33550.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttatt---ttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttat---tatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
                                                    |  ||   | ||||     ||  | ||| | |      ||   ||   |||||  | |    ||  ||| ||  |  |     |  |||| |  | |||          |||||  || |         |||||| |||||||| || ||||||| ||||||| | ||||| |||||||| |||||| | || ||||||||||| ||  | |||||||||||||||||||| || 
---------------------------------------------------gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

upper sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttgg-ggattgggggttctgagaattttttaattactgaattccacgcacgtg-gttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
                                                       ||   ||  |             |  |  |  |  || ||    ||   ||  | ||     || ||||   ||||  |  ||  |  |  |  |  |   | | | ||       |     ||||||||| || || |||||||||||||||||  ||||||||||||| || |||||||| || ||||| ||||| |||||||| || || || ||| | ||||| 
-------------------------------------------------------gtaagttgacagttggcaccgcctggtagacggtagc-gtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT

upper sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G064426_T02 (Zea mays), 3'ss of exon 2
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
                         |  |||      ||      | | |   |  | | || |||    |||||    |||  | ||  ||  ||    ||      |||      | |  |||||| || |     || | ||    |  ||||||  | | ||   |     ||||||||||||||| || ||||||| ||||||| | ||||| |||||||| |||||  | || ||||||||||| ||  | |||||||| ||||| ||||| || 
-----------------------gtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttggg-aattcagagtggcgtttcgcaaaccgcactttagcttaggt--ggggttttgtg-----ttgacttgtctacgtccacgttccttgtc--tgctgtttgcagGGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCC

upper sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S25_89V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
                                                  |  | |||| || | |||      | |  |||||||| ||   |  ||   |||||| ||| |             | |    |     ||   | | |  ||||  | || |            || ||| || || || || || |||  ||| ||||||||||| ||||||||||| |||||||| |||||||||   || |||||||||||||||||| | ||||||
--------------------------------------------------tgatggtttctttgatcatg----tgtacaatgtaaaact-tggcgtt---atttttgtttgtcc-----------tccctgcaccgcattgtctgccgttttccttg-accta-----------ttacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGATTTACTTTGGGCCATGAGCACATTAGGGTTTGAAGACTACGTCGAGCCG

upper sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S25_10V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
                                                                 |||   |  || |   ||||  |     | || |||  |   |  |   ||   ||| ||    ||  | || |||      ||  |  ||    | | |  ||      |  ||| || || || ||||| |||   || |||||||||||||| ||||||||||||||||| ||||| |||   || |||||||| ||||||||| | || |||
-----------------------------------------------------------------tcaccttagttctaggtgtattg-----gattcttaggtc--acgtacaggatgttgagg----tggaagttctttggcatttgtctgtcattttccttgacata-----tcacagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG

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|193425945|gb|FK385752.1|FK385752
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGAACAATCAATGGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGA-CAATCAATGGA
EST: gi|193648695|gb|FK600634.1|FK600634
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|33387515|gb|CA850722.1|CA850722
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|254330848|gb|GR842113.1|GR842113
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|13251995|gb|BG362898.1|BG362898
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|10845982|gb|BF071234.1|BF071234
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|58017783|gb|CX704525.1|CX704525
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|298167451|gb|HO012714.1|HO012714
EST:     GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|209715624|gb|BW674337.1|BW674337
EST:     GACACAATGCAAGAATGCGTTCCTGAATTCATCAGCTTCATTACCAGCGA                         GGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
EST: gi|58021138|gb|CX707880.1|CX707880
EST:     GTCTCAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGA                         GGAGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA
genomic: GACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagt ... tgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
           ttttaat  putative branch site (score: 3)
     agaattttttaattac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA