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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcttctctacatgccttaatcttttgatatctacttaaatatctcctagattggtattgataattgattgtactttgaaattgtgtttgttttgtaatattgaagtcaccaacctagttctttaatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG

Basic information

species Glycine max
transcript GLYMA09G01050.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 12
gtttgtgcttctctacatgccttaatcttttgatatctacttaaat--atctcctagattggtattgataattgattgtactttgaaattgtgtttgttt-tgtaatattgaagtca--ccaac--ctagttctttaatt-tgctttgacatt-------ttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG
   | |||  | ||| |   |    ||  ||| |   |||  | ||      |  |||  ||  ||  |     | ||   |||| |    |||||||||  | |  |  | || ||    |||  ||| |  | | ||  |||| | |  ||       ||  ||||||||| ||  |   |||||| ||  |||||||||| ||||||||||||||| | || ||  |||||||||| ||||||||||| |
--gtatgca-cactatagttccctgtcacttgttggatacccagattggaacctaagaacgggctttgtgg--aagtgatgtttgcagc-atgtttgtttacgaaccagcgcaggcagatgaacttctaatgatatgatcatgctcttatgtttgtatttttactcagGTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 5
gtttgtgcttctctacatgccttaatcttttgatatctacttaaatatctcctagattggtattgataattgattgtactttgaaattgtgtttgttttgtaatattgaagtcaccaacctagttctttaatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG
                                                  |||| | |  ||     |  ||   |   | | | |||||| ||||   |    || | |   ||   | |  ||   |   |  ||||     |||| | ||||||| ||  |    ||||||||| |||||||||||||||||||||| ||| | || ||| |||||||||| ||||||||||| |
-------------------------------------------------acctacagtattaggagcatctgggagatgtcttatattgtgattgt---ggctgatcgtatgtacttgcatgatttggtcgctgtctttttt-ctttgcttagGTTGGCAACCTTGCGGCTCCAGTAGAAGAATGGACTGTTGGTGGAACAGCATTGACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 12
gtttgtgcttctctacatgccttaatcttttgatatctacttaaatatctcctagattggtattgataattgattgtactttgaaattgtgtttgt--tttgtaatattgaagtcaccaacctagttctttaatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG
                                                     | | || ||   |||  ||   |   | | | | |||||||||   |  |  |||  |  |     |  || |   |   |||  |||  |  || | ||||||||| ||  |    ||||||||  |||||||||||||||||||||| ||| | || ||| |||||||||| ||||||||||| |
-----------------------------------------------------acagtgttaggaatacctgggagatatcttataatgtgtttgtgactgatcttatgtacttgcatgatttaatcgctgtcttttttttttc--ttggctcagGTTGGCAACCTTGCGGCTCCAGTTGAAGAATGGACTGTTGGTGGAACAGCATTAACATCACTGATGGATGTTGAGAGGAGGCACG

upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 12
----------------gtttgtgcttctctacatgccttaatcttttgatatctacttaaatatctcctagat-tggtattgataattgattgta---ctttgaaattgtgtttgtt-ttgtaatattgaagtcaccaacctagttcttt--aatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG
                | ||   | | | |  |    || |||  |     | |  ||  || | ||| | || |  |  || | || || |  |     |||  ||| | |      || || || | || | ||  | | |  | |||  ||||   | | |   | |  ||||||||||||| | | |||||||||  |||||||||||||||||||||||||  | || ||| | ||||||||||||||||| ||||
gttggttcttcattccgcttaatcatttttgtactttttgatcagtcttccttttttttcatttttccaatatctcattctgcttatagagttcaaactcttgttattctatcgaaggttatagtagttaa-taactgaacaaactttttgtaattgtttctcatcatgtcttcagGTTGGGAATCTGTCTGCTCCAGTTGAAGAATGGACTGTTGGTGGAACTGCCTTGACTTCATTAATGGATGTGGAGAGGAGACATG

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|4313688|gb|AI460807.1|AI460807
EST:     ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGACTAATATCATCA                         GTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGACTAATATCATCAgtttgtgctt ... ttttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|4313720|gb|AI460839.1|AI460839
EST:     ATGGTGCTGGAGCCCTNCTTCATAGTTGGAAGACTGGACTAATATCATCA                         GTTGGGGAATT-ATGTGCTCCAGTA
genomic: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGACTAATATCATCAgtttgtgctt ... ttttgatcagGTTGGG-AATTTATGTGCTCCAGTA
EST: gi|7284788|gb|AW597213.1|AW597213
EST:     ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGACTAATATCATCA                         GTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGACTAATATCATCAgtttgtgctt ... ttttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCA
EST: gi|4313349|gb|AI460468.1|AI460468
EST:     ATGG-GCTGGAGCCCT-C-TCATAGTGGGAAGACTGGACTAATATCATCA                         GTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCA
genomic: ATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGACTAATATCATCAgtttgtgctt ... ttttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatattgaagtcaccaacctagttctttaatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG
                                     ctttgac  putative branch site (score: 4)
                      tagttctttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcttctctacatgccttaatcttttgatatctacttaaatatctcctagattggtattgataattgattgtactttgaaattgtgtttgttttgtaatattgaagtcaccaacctagttctttaatttgctttgacattttgatcagGTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATG

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