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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgttttcatctctctagtttccttttctttcatgctacaactctcattgacatgtgaactattgaaaacttgatgttactgaatgtttatagtgttcaattcttgttgctttgtttgatttgctgatctgcatgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA

Basic information

species Glycine max
transcript GLYMA20G35530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35530.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g13890.2 (Oryza sativa), 3'ss of exon 2
gtatggtgttttcatctctctagtttccttttctttcatgctacaactctcattgacatgtgaactattgaaaacttgatgttactgaatgtttatagtgttcaattcttgttgctttgtttgatttgctgatctgcatgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
                                           | |||| || | | | |   || |     |||   ||| |  ||||  | ||   |  | ||| |   |    |   ||    |||    ||     | ||||| || || || ||||| ||||| || ||||||||||||||||||||| ||||
------------------------------------------gccactc-cactaata-gcacaccaacatgaacaaaatgctcatgaaaatgtaggtttcttaatgcaactaaactaaattatcatgcc---ctttgaacttgcagCTACGGCTACGACCCTTTTGGCCTCAGCAAGAAGCCAGAGGACTTCTCCAA

upper sequence: GLYMA20G35530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149428_T01 (Zea mays), 3'ss of exon 2
gtatggtgttttcatctctctagtttccttttctttcatgctacaactctcattgacatgtgaactattgaaaacttgatgttactgaatgtttatagtgttcaattcttgttgctttgtttgatttgctgatctgcatgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
                                  | |   |  ||  ||   | |   |||  |    ||||||  ||  |  | |  | ||| |  || |   |       |   ||| |            || ||  |  |||| ||||| || ||||| ||||| ||  |||||||||||||||||||||||||
----------------------------------tacggccgtcatttcctctagttttgttcatatatgaaaaactgcagagaatcgaagttaa-ggtatctgaactgaactatcttgctc-----------ctaca-actggcagCTATGGCTACGACCCTTTTGGCCTGGGCAAGAAGCCAGAGGACTTCGCCAA

upper sequence: GLYMA20G35530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G10340.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatggtgttttcatctctctagtttccttttctttcatgctacaactctcattgacatgtgaactattgaaaacttgatgttactgaatgtttatagtgttcaattcttgttgctttgtttga--tttgctgatctgcat----gcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
                                                           || |   | |      || ||||  ||   ||| | || ||   | || | | | || || || |  |||  || |||| ||       |||||||||||||||||||| ||||||||| | |||||||| ||| |||| || ||
-----------------------------------------------------------gtaagacactt----tttcatgtctctctttgtatgta-tgcctacttttggattctgtgcttaaggtttattggtctgaatctgaatttgcagTTATGGTTATGACCCATTTGGTCTTGGAAAGAAGCCTGAGAACTTTGCTAA

upper sequence: GLYMA20G35530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0089g01170.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtgttttcatctctctagtttccttttctttcatgctacaactctcattgacatgtgaactattgaaaacttgatgttactgaatgtttatagtgttcaattcttgttgctttgtttgatttgctgatctgcatgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
                            |    ||  ||      |  ||||      |||    | |  || |    |||  |   |  |  |  ||   | ||| || |    |||   ||||||| |  ||||  || |||||||||||||||||| || ||||| || ||||||||||||||||||||||||||
---------------------------gtaagattctatatatatatcctcaactttgtgtttgttttccaagaaaacatgagaaaaacagactgaagaagtgaatgctgggaaattttgctgatttgtt--tctg--tggctgcagTTATGGTTATGATCCTTTTGGGCTCAGCAAGAAGCCAGAGGACTTCGCCAA

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|209727197|gb|BW655235.1|BW655235
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGCGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|209707832|gb|BW683728.1|BW683728
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|209697500|gb|BW670001.1|BW670001
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|15284925|gb|BI468816.1|BI468816
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|24135389|gb|BU925899.1|BU925899
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|31305455|gb|CD390658.1|CD390658
EST:     CGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: CGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|15662304|gb|BI699675.1|BI699675
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|9898921|gb|BE607889.1|BE607889
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|213597770|gb|DB960327.1|DB960327
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGCGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|19270057|gb|BM886313.1|BM886313
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|31561294|gb|CD487132.1|CD487132
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|17962784|gb|BM269541.1|BM269541
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|23064373|gb|BU579146.1|BU579146
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|31561507|gb|CD487345.1|CD487345
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|15286458|gb|BI470349.1|BI470349
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|8670142|gb|BE191249.1|BE191249
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|192293843|gb|FG986052.1|FG986052
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|213612114|gb|DB956851.1|DB956851
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|17401712|gb|BM178494.1|BM178494
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|209715030|gb|BW650881.1|BW650881
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|8670152|gb|BE191259.1|BE191259
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|13562573|gb|BG550793.1|BG550793
EST:     CCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: CCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|20813004|gb|BQ297482.1|BQ297482
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|17518866|gb|BM187908.1|BM187908
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|31474651|gb|CD416679.1|CD416679
EST:     GAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGTTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: GAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|15285366|gb|BI469257.1|BI469257
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|31470087|gb|CD412115.1|CD412115
EST:     CCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: CCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|213595532|gb|DB962430.1|DB962430
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
EST: gi|213595421|gb|DB962403.1|DB962403
EST:     TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGA                         TTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
genomic: TTGGACCGATCAGAGATCCCCGAGTACTTGACCGGAGAAGTGCCTGGAGAgtatggtgtt ... atgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagtgttcaattcttgttgctttgtttgatttgctgatctgcatgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA
                                  tgctgat  putative branch site (score: 3)
                           tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtgttttcatctctctagtttccttttctttcatgctacaactctcattgacatgtgaactattgaaaacttgatgttactgaatgtttatagtgttcaattcttgttgctttgtttgatttgctgatctgcatgcctgcagTTATGGTTATGACCCGTTTGGTCTTAGCAAGAAGCCAGAGGACTTCGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA