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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG

Basic information

species Glycine max
transcript GLYMA16G33380.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 4
gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctt--tattgtgaaacttaata---actctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG
                                                    |||    |  | || ||  |      |  |  ||  ||   ||  |||||  || | |    |   |  ||     | | | |  |  || |||   | ||| ||   | |||   | |||| |     | |   ||||||||||||||  |||| || || || || ||||||||||| ||||| ||||||||||||||  || | |
---------------------------------------------------gtatgtggaacgttagatgttttctctctgttgag--tactactgatgaaattattagtctgatgtgttaaattgccaatattttctgctaatgtatgaattagtacttaatctaactttcttgtcactctttg-gcagTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAG

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 4
gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG
                                                                          |    ||| || | ||  || |        | | ||| | |||  |  |  ||   |  |||  |  ||| |  | |||||        | | | | |||  |  || ||||||||||||||  |||| ||||| || || |||||||| |||||||| || |||||||| ||  ||||||
-------------------------------------------------------------------------aatgaaactgcacg-tagctcctaaaccttgagctcttttcttagccctattctcgatg-ctcagtcctgt-attcctaata-------ctttatgagttg--tccatgcagTCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTG

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 4
gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG
                                                                               || |     |||  | |   | |        | || |||| |   |  ||  |  |   | ||||||  |  |   |||   ||    || | |  |  | | ||||||||||||||| ||||||| || ||||| ||||||||||| ||||| || |||||||||||  |||| |
-------------------------------------------------------------------------------acccgtatatataccctaccatatt----tgtgtgctaatgtgcagtcta--tggttcatgttgtgagtcccatgtacttaattgtggttgtgtttaaatgtgcagTCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G069765_T02 (Zea mays), 3'ss of exon 4
gtat-ttgtatcttttgcttcgctttattgatattgctttgtcacacatacattataca--tactgc-tatatactgcactgcactcca-ggctatgtcttgtgaaagcatcacttctgt---taatctaaggcttagtttc-tctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG
||||     ||  | |   | ||||   ||     |  |  | |   |   || |  ||   |   | ||| |  | |  |    |  | || | ||| ||| || | |  ||  | | |   ||||   | |   ||| |  | | | |||  |  |  |   ||    ||    || | | |||||   ||||||||||| ||| ||||||| || || || ||||||||||| ||||| || |||||||||||  |||| |
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagacc-ccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtg--cagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
gtat-ttgtatcttttgcttcgctttattgatattgctttgtcacacatacattataca--tactgc-tatatactgcactgcactcca-ggctatgtcttgtgaaagcatcacttctgt---taatctaaggcttagtttctctt-tattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG------------------------------
||||     ||  | |   | ||||   ||     |  |  | |   |   || |  ||   |   | ||| |  | |  |    |  | || | ||| ||| || | |  ||  | | |   ||||   | |   ||| |   || | |||  |  |  |   ||    ||    || | | |||||   ||||||||||| ||| ||||||| || || || ||||||||||| ||||| || |||||||||||  |||| |                              
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagacc-ccatatatatacctaattgtatgtgcagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtg--cagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG
                                                                     | |    |    |  |   | | |||  ||         ||||||| |||       |||||| |||   | | ||  |  |  ||  | ||  | | |||| |     |  |||||| |||||||||||||| ||||| ||||| ||||||||||| |||||||| || || |||||  ||||||
---------------------------------------------------------------------atttttttagcttttaaattttttctgttggg-------cttctgtcaat-------ttagttcctcaaaactctgtcatct--tagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG

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|16276828|gb|BI942066.1|BI942066
EST:     ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAG                         TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
genomic: ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAGgtatttgtat ... atgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
EST: gi|16281961|gb|BI944761.1|BI944761
EST:     ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAG                         TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
genomic: ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAGgtatttgtat ... atgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
EST: gi|193636212|gb|FK580749.1|FK580749
EST:     ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAG                         TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
genomic: ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAGgtatttgtat ... atgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
EST: gi|16278542|gb|BI942959.1|BI942959
EST:     ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAG                         TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
genomic: ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAGgtatttgtat ... atgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
EST: gi|24206236|gb|BU965489.1|BU965489
EST:     ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAG                         TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
genomic: ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAGgtatttgtat ... atgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
EST: gi|162286128|gb|FC456630.1|FC456630
EST:     ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAG                         TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA
genomic: ATGGGAATGCTATCTTACGTGAATTAGACCTTGCTCACCCTGCTGCAAAGgtatttgtat ... atgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG
                    taataac  putative branch site (score: 1)
                                     ttatttgaatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA