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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttttcatatgttgatttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG

Basic information

species Glycine max
transcript GLYMA17G36620.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g08400.2 (Oryza sativa), 3'ss of exon 10
--gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttttcatatgttgatttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG
   |||   |          |        |  ||  ||   |   |  |  |   ||||    | |  |  |       | ||||| || || || |  ||| ||| | || || |||||  |||||||||||||||||||||| ||| |||| |||||||
tacaatatgcaaattatttgttgtgttatcatttggttcttctgta-ttgggacctcatgaagt-acattgtcggtattttaatgtgttattgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCGTGGTTGCGACTTAAAG

upper sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G017845_T01 (Zea mays), 3'ss of exon 10
gaatcctccctccccccatc-ccccaccccgttcc---tttcacaacaactttgttttcatatgttgatttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG
   | ||||    ||   |           ||||    ||    ||  | |  |  | |  |  ||  |||  | ||  | |  ||| | |||| || |  ||| ||| | || || |||||  |||||||||||||||||||||||||| ||||||||||||
---ttctcctataccatgttgttttgtttggttctacattgttgaatcattaaggatgctcaaatttgttt-gtatagacttttatggtgttttgttcttgcagATTGTTGACAGGTTCAATTTTAGCTCATGAGATGATGCATGCATGGTTGCGGCTTAAAG

upper sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 9
gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttt-tcatatgttg-atttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG
                        |      || |||  |  | | |   ||  || |||||   | ||||   |   |||  | |  |    |||  ||||||| |||||||| || || ||||||||||||||||||||||| ||| || |||| ||||
--------------------gtaaaaaagactctttttgcttccattgaattgatcttatgtcacagttcaagcattgatggttttgctgaattttgttcagGTTACTTACTGGTTCGATTCTAGCTCATGAGATGATGCATGCGTGGATGAGGCTCAAAG

upper sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 10
gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttttcatatgttgatttcatttacccatgaatgt---ttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG
   |  |           |  |  |         |  |   |||  ||   |||  | | |||  |  |||| |  ||| | ||      | | | |   ||||||||| ||||| || ||||| ||||| |||||||||||||| ||||| || || || |
--tttttgttaaaaatggtggcagaagataagtatgccctcaca-tttgagttttgtttcttggataaattttctaatgtaagtaaacactctttgtatacagGTTGCTAACTGGGTCGATCCTTGCTCACGAGATGATGCATGCCTGGCTCCGACTAAATG

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|58025122|gb|CX711863.1|CX711863
EST:     ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAG                         GTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCG
genomic: ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAGgtaacaattt ... cttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCG
EST: gi|208239934|gb|GE042702.1|GE042702
EST:     ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAG                         GTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCA
genomic: ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAGgtaacaattt ... cttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCA
EST: gi|13789572|gb|BG652163.1|BG652163
EST:     ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAG                         GTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCG
genomic: ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAGgtaacaattt ... cttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCG
EST: gi|193391644|gb|FK356501.1|FK356501
EST:     ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAG                         GTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCA
genomic: ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAGgtaacaattt ... cttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCA
EST: gi|105634612|gb|DW247614.1|DW247614
EST:     ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAG                         GTTGCTTACTGGATCACTCCTAGCTCATGAGATGATGCATGCATGGCCGCG
genomic: ACTACACGCTGCGATGTGACCGCAATTCTCGTTTTATATGGTCTTCCAAGgtaacaattt ... cttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttttcatatgttgatttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG
             tgttgat  putative branch site (score: 4)
                                    tgtttttttcttttct  putative PPT
                                  aatgtttttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatcctccctccccccatcccccaccccgttcctttcacaacaactttgttttcatatgttgatttcatttacccatgaatgtttttttcttttctcagGTTGCTTACTGGATCAATCCTAGCTCATGAGATGATGCATGCATGGCTGCGGCTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- atcctcc
- - - - -ctccccc
- - - - - - - - -atccccc
- - - - - - - - - - - - -ccccgtt
- - - - - - - - - - - - - - - - - - -cacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgaa