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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

Basic information

species Glycine max
transcript GLYMA07G39380.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
gtttgtgc-ctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaat--actgggtccatcaactcaattttt-------tgatt-tgctatgatatt-------ttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
|| ||  | ||||  |   |      |  |   ||   || ||| ||     | |    |  || |||   ||     |||  | ||  ||||||| | |   ||  |  |   ||  | || || |       ||||  |||| | || ||       ||  ||||||||| ||  |   ||||||||| ||||||||||| ||||||||||||||| | || || |||||||| || |||||||| || |
gtatgcacactatagttccctgtcacttgttggatacccagattggaa----cctaagaacgggctttgtggaagtgatgtt-tgcagcatgtttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttttactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 5
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                               |   |    |||||     |||   ||||   || || ||  ||||||||| | |   | | |  |   |   | |       ||   ||||||               |||| | ||||||| ||  |    ||||| |||||||||||||||||||||||||| ||| | || ||| ||||||| || |||||||| || |
-------------------------------acctacagtattaggagcatctgggagatgtcttatattg--tgattgtggctgatcgtatgtacttgcat--gatttggtcgctgtctttttt--------------ctttgcttagGTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 12
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                                   |     ||||  ||  ||   ||||   || |||||  || |||||  | |   | |       |||| |    ||  | ||  | | ||  |||  |       || | ||||||||| ||  |    ||||| || ||||||||||||||||||||||| ||| | || ||| ||||||| || |||||||| || |
-----------------------------------acagtgttaggaatacctgggagatatcttataatg--tgtttgtgactgatcttat------gtacttgcatgatttaatcgctgtctttttttttt------cttggctcagGTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctaga--ttggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                                    |  | |     |||||  ||| |   || |||  ||   ||||  |  |    |   |||||||| ||| |    ||   || |   |   |||  | ||   ||||  |  |||||||| || ||   ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| |
---------------------------------gtttgtactccaccatttccactaaaatctgttttccatctgtgatcataat----agcctttggtaa-actag---tatgtgcttagaatga-gatgagttaacttattg-gcgcagGTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
--------------------gtttgtgcctatgctcttcacattatcttctaatcatcaaatta----gatatttcttctagatt---ggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttt-tgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                      |  |   | | || ||       |||||   |  |   |||      |||| || |   | ||   |  || ||    |  || |  |    || |||   || || |   |   | |||  | ||||| | |||   | | ||  | |  ||||||||| ||| | | |||||| || ||||||||||||||||||||||||||  | |||||||| ||||| ||||||||||||||||
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggtt--atagtagttaataactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG

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|13788196|gb|BG650788.1|BG650788
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|254342635|gb|GR858797.1|GR858797
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|254342634|gb|GR858796.1|GR858796
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|298174798|gb|HO017907.1|HO017907
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|151402902|gb|EV272715.1|EV272715
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|26058870|gb|CA801784.1|CA801784
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|254318250|gb|GR832418.1|GR832418
EST:     TGGTGCTGCAGCCCTCCTTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: TGGTGCTGCAGCCCTCC-TTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|58023377|gb|CX710118.1|CX710118
EST:     GCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: GCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|18712744|gb|BM522681.1|BM522681
EST:     ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCG                         GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGATTAATATCATCGgtttgtgcct ... ttttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG
                           ttttgat  putative branch site (score: 4)
                     tcaattttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcctatgctcttcacattatcttctaatcatcaaattagatatttcttctagattggttttaatgattgattgtggttcaaaatgtttggtaatactgggtccatcaactcaattttttgatttgctatgatattttgatcagGTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA