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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgtttgtgtaaataattgcacgagttctttcatatattttggaaactacatgctgtgggcttacattgtatgttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG

Basic information

species Glycine max
transcript GLYMA13G33260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G33260.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G170088_T03 (Zea mays), 3'ss of exon 6
gtttgtttgtgtaaataattgcacgagttctttcatatattttggaaactacatgctg-tgggctta-cattgtatg-ttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
|| ||||  ||  |    ||  | |  |    | | |  ||| |     |   || || ||   |   |||   |   || | ||| ||           ||| |||||| |  ||||| |  | || ||||| || ||||| |||||||||||||||| ||||||||||
gtatgttcatg--atctctttgatgtttcacatgaaacctttcgatttttgtttgttggtgaaatcggcatctaacaattgtgccacatatttttt-tgacagTGATGATAATGTTGACATGAATCTGGAGGATATGATGGTTATGGAAGCAATTTGGCGTTCCATTCAG

upper sequence: GLYMA13G33260.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007288_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------gtttgtt-tgtgtaaataattgcacgagttctttcatatatttt----ggaaactacat---gctgt-gggcttacattg-----ta--tgttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
                                                                    ||||    || |||||| || |   |  |   || | || |||    |   | |||||    |||| | | | | || |     ||  |  | | |||  ||          ||| |||||| |  ||||| |  | || ||| |||| ||||| |||||||||||||||| ||||||||||
gtatgttcatgctatctcttttatgtttcacatgaaaccattctatttttgtttgttgtaacttacaatttgcaacgtttaaata-ttacggaaacttgatcttttagttttacagtggattacatttaactgttgagatgaaatcgacatctaactactgtgccacctgtttttgctgacagTGATGATAATGTTGACATGAATCTGGAGAACATGATGGTTATGGAAGCAATTTGGCGTTCCATTCAG

upper sequence: GLYMA13G33260.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17145.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttgtttgtgtaaataat-tgcacgagttctttcatatattttggaaactacatgctgtg-ggcttacattgtatgttctcccaa-----atgcggaaaactg--cagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
      | |   || | || ||||| |   |  | |||  | ||||||  |  |  ||| | || | | ||    ||              ||  ||||||||   ||| || | | | |||||| |||| ||||| || || ||||||||||||||||| |||||||| || |||
------tggctaaagttatatgcacaa---cggtaatacgtgttggaactttgaatctgagtggttcatatcaggtgactgatatgtggttatctggaaaactcttcagGGACGGTCAGTTTGACTTTGATCTTGAAGATATAATGGTCATGGAAGCAATATGGCTTTCGATGCAG

upper sequence: GLYMA13G33260.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G78420.2 (Arabidopsis thaliana), 3'ss of exon 8
-gtttgtttgtgtaaataattgcacgagttctttcatatattttggaaactacat-gctgtgg-gcttacattgtatgttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
  ||| ||||| |   |  |||   ||| |   | ||||        |   || | |   ||  |  |   |  ||| ||             ||  || ||| || |||||  |||||||||||||||||||  | ||||||||||||||||| ||||| ||  |||||
actttttttgttttgttttttg---gagctaagtgatatgaacacagattcacttagaaatgaagagtgattcatatatttgatttgtctataaactcttcagGGAGGATGAGGTTGACGTTGACCTTGAGGAATTGATGGTCATGGAAGCAATATGGCTCTCTGTTCAG

upper sequence: GLYMA13G33260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0093g00620.t01 (Vitis vinifera), 3'ss of exon 6
-----gtttgtttgtgtaaataattgcacgagttctttc-atatattttggaaactacatgctgtgggcttacattgtatgttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
      ||  ||||  |   |  ||  || |||   ||  || |  ||    |  | | || | ||      |||| ||   |      | ||     || ||||| ||||| ||||||||  | || |||||||| || ||||| |||||||| || |||||||||||||||
gttctattgatttggctctgttttta-acaagtcaattagatgtgcttattgatttgcttggtatgccacagcattata-actaatttgattgt----aaatgcagGGATGAGGAATTTGATCTGGATCTTGAGGATATTATGGTTATGGAAGCTATCTGGCTTTCCATTCAG

upper sequence: GLYMA13G33260.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S333_57V6.2 (Physcomitrella patens), 3'ss of exon 6
gtttgtttgtgtaaataattgcacgagttctttcatata----ttttggaaactacatgctgtgggcttacattgta--tgttctccca--aatgcggaaaactg-cagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
        ||  | | |  | ||  |  | | | | | |    | |     |  | |     | || | |  | | |  ||||||  |    ||  |      || |||||||||||| |||||  |||| || |||||||| ||||| ||||| ||||| ||||| || ||||||
--------gtacacaaagcttcaaaacgtttcttagaaaagattctcaagtatgagaccaaattggatcatctgggacttgttctgacgttgatctgtggttatgtcagAGATGATGACTTTGATCTTGATCTCGAGGACATTATGGTAATGGAGGCAATATGGCTCTCTATTCAG

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|254342559|gb|GR858721.1|GR858721
EST:     ATCAGTGGTTAGAGCAAATGCAACCACTAGGACCAATAG                         AGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAAT
genomic: ATCAGTGGTTAGAGCAAATGCAACCACTAGGACCAATAGgtatgctagc ... aaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAAT
EST: gi|254325782|gb|GR838663.1|GR838663
EST:     ATCAGTGGTTAGAGCAAATGCAACCACTAGGACCAATAG                         AGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAAT
genomic: ATCAGTGGTTAGAGCAAATGCAACCACTAGGACCAATAGgtatgctagc ... aaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAAT
EST: gi|17964440|gb|BM271175.1|BM271175
EST:     TCATGTGCCACATCAGTGGTTAGAGCAAATGCAACCACTAGGACCAATAG                         AGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAAT
genomic: TCATGTGCCACATCAGTGGTTAGAGCAAATGCAACCACTAGGACCAATAGgtatgctagc ... aaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactacatgctgtgggcttacattgtatgttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG
               ggcttac  putative branch site (score: 3)
                  ttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttgtgtaaataattgcacgagttctttcatatattttggaaactacatgctgtgggcttacattgtatgttctcccaaatgcggaaaactgcagAGATGATGAATTTGACGTTGACCTTGAGGACATCATGGTCATGGAAGCAATTTGGCTTTCCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- -tgtttgt
- - - - - - - - - -tgcacga
- - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttaca