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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttggagagagtagttggttttcttttatggaattctctgattgatttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT

Basic information

species Glycine max
transcript GLYMA09G37020.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37020.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 5
gttagtgttggagagagtagttggttttcttttatggaattctctgattgatttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
          | ||| ||  |   | | || ||      | |||| ||    | || ||    || |   |   | | | || ||  |  |             ||||| || ||||||||||| ||| ||||||| |||||||| ||||||||  | || ||| | || || ||| |  | ||||| |  |||||  | ||||| |
----------gtgagtgtgatctttgtactatttccttttcctctaatgctatcatatgc--ctatttattaaccaaaaatttatccgtgacctc-----tactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT

upper sequence: GLYMA09G37020.3 (Glycine max), 3'ss of exon 5
lower sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagtgttggagagagtagttggttttcttttatggaattctctgattgatttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
                   ||  |||  || | |    ||| ||   || |    |    ||  | ||  ||    | | ||| |  |   |       ||  |||||| ||||| |||||||||||||| || || || |||||||| |||||||| || ||| |||| |||||| |  | |||||||||| ||| ||| || | |
-------------------gtcagtt--ctgtaacattattgtcctttttacagttggaaagagagtatgtgtctcaaatttattccgactt------gtctggcagGTATCTCTGTTCTTCACTGAGTCCCCGACAAACCCATTCCTTAGATGTGTCGACATTGAGCTAGTTTCAAAAATATGCCACAAGAGGGGAACTCTGGTTT

upper sequence: GLYMA09G37020.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 5
gttagtgttggagagagtagttggttttcttttatggaattctctgattgatttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
|| ||| ||  |||  || ||| |||||  |  | |   |  | | | | ||   |||  |  |   || |  |   ||| | |  ||  ||| | ||  | |||||||  | || ||||||||||||||||| ||||||||||| || ||||||||||| ||| || ||||||||||||||||||||| ||||||  |  |  |||
gtcagtattcaagatggttgttagtttt--tcgaagttttcttttcagtaatcatttttcaaatggcaggtcatactgagatgac-tgacattgt-ca--catgcagGTTACACTTTTCTTCACTGAGTCTCCGACCAATCCATTTCTCAGATGTGTTGACATTGAGTTGGTTTCAGAGCTTTGCCACAGGAAGGGAGCACTAGTCT

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|16346611|gb|BI972206.1|BI972206
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|17964323|gb|BM271060.1|BM271060
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|18712556|gb|BM522662.1|BM522662
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|7796714|gb|AW782108.1|AW782108
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|208077881|gb|GD874825.1|GD874825
EST:     TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TTGATCCAGCAGATGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT
EST: gi|18720947|gb|BM523284.1|BM523284
EST:     TGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAAT                         GTGTCTCTATTCTTCACTGAGTCGCCTACCAATCCATTCCTGAGATGTGTT
genomic: TGTTGGAGCCTTGGAATCTGCATTGGAGCAGCACAATgttagtgttg ... aatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT
                          agttaat  putative branch site (score: 4)
                            ttaatatggtattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgttggagagagtagttggttttcttttatggaattctctgattgatttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG