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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctggaggtgctggttcctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA

Basic information

species Glycine max
transcript GLYMA19G22730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 4
--------------------ttgctggaggtgctggttcctcgaaaaccagagggt---ttgaac---ctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA
                    ||    ||  |  ||      |  | | ||  | ||    | ||    | | |  | |||   | |||| ||  || ||    ||  || |      | ||   ||||||||||||||||| ||||| ||||| |||||    ||||| || ||||| ||||| ||||| || ||||| ||||||||||| |||||||||||| | 
gtttgtgaaacatatgcatattttgtgaactattgcagtaacatacatcattgtgtaacataaatatgccatcttttatatggataattgttggttcttacaattgattaaccgatttttttgcagTGGTGGCTACAACATTAAGACTGGACCAGGCTGCAGTATTGAGCTGATGAAGTTTGACATGGGAGGCTCTGCAGCAGTTTTTGGTGCAGCAAAAGCTTTG

upper sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
-ttgctggaggtgctggtt--cctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA
 |  ||     | |||  |  | | |||    |    |||   | ||   |    |  ||     ||||  | ||| ||  |||     |    |||    ||||||||||||||||| ||||| ||||||||||| |  ||||| || |||||||| || ||||||||||| ||||| ||| |||| || || |||||| | 
gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT

upper sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
ttgctggaggtgctggttcctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA
 | || ||| || ||| | ||         |  |  |  | |     | |  ||||    |||  |  |||  |   |  ||||       ||||   || |||||||||||||| || || || |||||||| || ||||| || |||||||| |||||||| ||||| ||||| ||| |||| || ||||||||  | 
gtactagagctgttggcttct-----gtttgccgcatcaatctctttatt--taatacttattagttattgaccagatggtttt-------tgttcacagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT

upper sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 4
-ttgctggaggtgctggttcctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttat-ttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA
 ||| |          ||  |  | | |  |     | | |   |     |   | |  | || | |   |||||||     ||||| || |||| | ||||||||||||||||||||||||| |||||||||||||  ||||| || ||||| ||||||||||| ||||| ||||| ||| | || |||||||||||  | 
tttgttttcaaaa--agtggccagtataataatctatgttattatgtgcatttgattctccatctatacgtgttcttaaacatttatctttcatggttttagTGGTGGCTACAACATCAAGACTGGACCTGGCTGTTCTATTGAGCTCATGAAGTTTGATATGGGGGGTTCAGCTGCGGTTCTCGGTGCAGCAAAAGCCATT

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|254323478|gb|GR835924.1|GR835924
EST:     CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
genomic: CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
EST: gi|192311508|gb|FK005239.1|FK005239
EST:     CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
genomic: CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
EST: gi|8282655|gb|BE020216.1|BE020216
EST:     CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
genomic: CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
EST: gi|192311498|gb|FK005229.1|FK005229
EST:     AGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
genomic: AGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
EST: gi|193435123|gb|FK400267.1|FK400267
EST:     CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAAC
genomic: CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAAC
EST: gi|192311499|gb|FK005230.1|FK005230
EST:     CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
genomic: CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
EST: gi|192311507|gb|FK005238.1|FK005238
EST:     CAAG-TAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
genomic: CAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAA
EST: gi|193424866|gb|FK388181.1|FK388181
EST:     CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAG                         TGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTG
genomic: CCTGTCAATGTCAAGTTAGCATTAGTCGGAAAAGGTTTGACTTTTGATAGgtacttaatt ... atgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA
 acctaac  putative branch site (score: 2)
                tttttctttgttcttt  putative PPT
     aataattacaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctggaggtgctggttcctcgaaaaccagagggtttgaacctaacagtaataattacaatttttctttgttcttttttttttatttgcatgttattagTGGTGGCTACAACATCAAGACAGGACCTGGCTGTTTGATTGAACTTATGAAATTTGATATGGGCGGTTCTGCTGCAGTTTTTGGAGCAGCAAAAGCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - -ggaggtg
- - - - - - -tggttcc
- - - - - - - - - - - gaaaacc
- - - - - - - - - - - - - - - - gggtttg
- - - - - - - - - - - - - - - - - - - - -cctaaca