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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttcttcttctagcaatggtttgtctggaaatatagttttttgttagcttttgaagcttgttgttaatctatatgctgctgaattaattcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTTGAAGAAATGGATGCAGATTAATGGACTAGAAATGTTTATTTCAAAGTTG

Basic information

species Glycine max
transcript GLYMA19G17920.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G17920.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 3'ss of exon 9
---tgtttcttcttctagcaatggtttg-tctggaaatatagttttttgttagcttttgaagcttgttgttaatctatatgctgctgaattaattcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTTGAAGAAATGGATGCAGATTAATGGACTAGAAATGTTTATTTCAAAGTTG
      |  | | |    |     | || ||   | |   | |  | | | | |||   | ||  || | | |   ||    |  |  |||  ||  ||  ||||| || ||||| ||| | ||   ||| |||||||| || ||||||||||| |||||||||||||||||||| | |    ||  |    |||     ||  
ttgaactcatccctgcctcccccatctgctcccaacagggaatgctatttcatcttactatgcacgtggatga---atgatttattttattg-ttgcttcccagGTTCCTGATGACCTTTTAGAGGAAGCCAAGGCAGCAGCTAAAGCAGCTCTGGAAGAAATGGATGCAGATTAGTTGGACGGACCTAAGCATTCATGGGTCC
















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|31472889|gb|CD414917.1|CD414917
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|151406675|gb|EV276490.1|EV276490
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|151405011|gb|EV274825.1|EV274825
EST:     AATTAGAGGTGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTATCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGTTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|192334683|gb|FK025888.1|FK025888
EST:     AATTAGAAATGAGCTGGGTGTGTAATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|15203950|gb|BI426727.1|BI426727
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|151411404|gb|EV281215.1|EV281215
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         -TACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|151409103|gb|EV278911.1|EV278911
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCGACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAG
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAG
EST: gi|31456760|gb|CD398788.1|CD398788
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|21676130|gb|BQ628481.1|BQ628481
EST:     GATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: GATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|8403145|gb|BE058779.1|BE058779
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|192325978|gb|FK016655.1|FK016655
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCA-CATGAGAAA                         GTACCAGATGAGCTTCTTGAATT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATT
EST: gi|16344394|gb|BI969989.1|BI969989
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|7685409|gb|AW756057.1|AW756057
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGNCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCGNAGGCAGCGGGCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|16344458|gb|BI970053.1|BI970053
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|254321256|gb|GR827705.1|GR827705
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTC
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTC
EST: gi|207747548|gb|GD720253.1|GD720253
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAAATTAGCAAAGGCA
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAA-TTAGCAAAGGCA
EST: gi|193712489|gb|FK649652.1|FK649652
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGACTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAG-CTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCT
EST: gi|254321257|gb|GR827706.1|GR827706
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
EST: gi|26047788|gb|CA784463.1|CA784463
EST:     AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGA
genomic: AATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGA
EST: gi|16104849|gb|BI892589.1|BI892589
EST:     GAATCAAACCGCCAACATGAGAAG                         GTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT
genomic: GAATCAAACCGCCAACATGAGAAGgtaaggctgg ... tcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcttttgaagcttgttgttaatctatatgctgctgaattaattcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTTGAAGAAATGGATGCAGATTAATGGACTAGAAATGTTTATTTCAAAGTTG
                                      aattaat  putative branch site (score: 3)
                                            ttcttttac  CT-rich tract
                                    tgaattaattctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttcttcttctagcaatggtttgtctggaaatatagttttttgttagcttttgaagcttgttgttaatctatatgctgctgaattaattcttttacagGTACCAGATGAGCTTCTTGAATTAGCAAAGGCAGCGGCCAAAGCAGCTCTTGAAGAAATGGATGCAGATTAATGGACTAGAAATGTTTATTTCAAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - -cttcttc
- - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgctgc