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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgtttgtgttattagctcagagtttctcagggacaccatgcctaatctcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG

Basic information

species Glycine max
transcript GLYMA17G01550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g53230.1 (Oryza sativa), 3'ss of exon 2
---tgcat-gtttgtgttattagctcagagtttctcagggacaccat--gcctaatctcattga-ttgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG
   ||| |  ||||     |||||  ||   ||  ||   |  | |    | |  | |  | || || |    | ||  ||  |  | |  |||      ||| ||| ||||| || |||||||| ||||| ||||| ||||| |||||| ||| ||| |||||||| || ||  | ||||| ||||||||||| ||||| ||| ||
gtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttgaacactatgtcaatattctgagaatttcttacagTTATACCGGTGAAGATGGGTTTGAAATCTCTGTTCCATCAGAGAATGCAGTTGATCTTGCAAAGGCCCTCCTGGAGAAATCTGAAGGCAAGGTGAGACTG

upper sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G876898_T01 (Zea mays), 3'ss of exon 2
tgcatgtttgtgttattagctcagagtttctcagggacaccatgcctaatc-tcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG
                                |      | || | | |||  ||||  |||  |  || ||  |||   ||   | |||     |||||| || || || |||||||| ||||||||||| ||||| |||||| ||| ||| ||||||||  | || || || || | ||| ||||| |||||  |  ||
------------------------------gtatcacttcgattctttatcgccattatttgagc--agtattgtaaggattgtcttatttcttatttcagCTACACCGGCGAAGATGGTTTTGAGATCTCTGTTCCGTCAGAGAATGCAGTGGATCTTGCAGAGGCCATCCTAGAGAGATCGGAAGGCAAGGTGCGGCTG

upper sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G11860.1 (Arabidopsis thaliana), 3'ss of exon 3
-------tgcatgtttgtgttattagct------cagagtttct-----cagggacaccatgcct-------aatctcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG
       | |||||||    |||  |||      |||| || ||     || | | || ||  ||       ||      |||   |  ||    |||| |   | ||| | || ||  |||||||||||| ||||||||||| |||||||| || |||||    |||||||  || ||||| || ||||||||  |||| || || || || ||||||||  | 
gtaaaatttcatgttt-cactatctgcttctagtcagatttgcttggttcaagtagacaatagctcaagaggaaaagttctgaagatctcataggtaatgaatgtctct-gttttggtttttcagGTATACCGGGGAAGATGGGTTTGAGATTTCGGTTCCAGATGAGCATGCTGTGGATCTAGCAAAAGCAATCTTGGAGAAGTCCGAGGGTAAGGTAAGGCTT

upper sequence: GLYMA17G01550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g01540.t01 (Vitis vinifera), 3'ss of exon 2
tgcatgtttgtgttattagctcagagtttctcagggacaccatgcctaatctcattgattgtaccaagcataataaccttttcttgattggga--ctttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG
   ||| ||  || |  |   || | |     | |   ||  |    |    ||        | ||||     | |  ||||||| |   | |   ||||||||| || || |||||||||||||| || ||||||||||| ||| ||| |||||||||||||||||||||  |||| |||||||||||||||||||| || 
-taatgatttagtcac-aatccaaattgcaatatgatgactgtctgaatcaacaaaccccacaacaagacacttgatattttctttacacgaaaattttcagGTACACAGGTGAAGATGGATTTGAAATTTCAGTTCCTTCCGAGAATGCAGTAGATCTTGCCAAAGCAATCTTGGAGAAATCTGAAGGGAAGGTAAGGTTA

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|7692090|gb|AW760205.1|AW760205
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|11413669|gb|BF425680.1|BF425680
EST:     TTACCAGGACACG                         ATATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|20815044|gb|BQ299522.1|BQ299522
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCACGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|17400633|gb|BM177415.1|BM177415
EST:     GTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: GTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|120530557|gb|EH258690.1|EH258690
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|120534357|gb|EH262490.1|EH262490
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAG
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGG-AAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAG
EST: gi|15663317|gb|BI700688.1|BI700688
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|22929190|gb|BU546329.1|BU546329
EST:     ACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATNNCAGTTCCTTCAGAGCATGGAGT
genomic: ACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|31561841|gb|CD487679.1|CD487679
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|37996377|gb|CF807966.1|CF807966
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|120533743|gb|EH261876.1|EH261876
EST:     TCCGTGTGTTGGACCATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGA
genomic: TCCGTGTGTTGGAC-ATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGA
EST: gi|27424988|gb|CA936508.1|CA936508
EST:     TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGG                         GTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
genomic: TTCCGTGTGTTGGACATCAATGGCTCAGAGTGTTTTCTTACCAGGACAGGgtatgctttt ... ggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGT
EST: gi|31306665|gb|CD391868.1|CD391868
EST:     TACCAGGACA-G                         GTAATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAG
genomic: TACCAGGACAGGgtatgctttt ... ggactttcagGT-ATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatctcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG
                                                ctttc  CT-rich tract
                        ataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatgtttgtgttattagctcagagtttctcagggacaccatgcctaatctcattgattgtaccaagcataataaccttttcttgattgggactttcagGTATACTGGGGAAGATGGATTTGAGATCTCAGTTCCTTCAGAGCATGGAGTAGATCTTGCCAAAGCAATACTGGAAAAATCTGAAGGGAAGGTAAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG