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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaactcacttccaacattttctcagtgtttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC

Basic information

species Glycine max
transcript GLYMA13G19650.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19650.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g30730.1 (Oryza sativa), 3'ss of exon 2
gtaccaactcacttccaacattttctcagtgtttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC
                          |    |   | | ||  | |  ||  | || || ||   | ||| || |      |||         |   ||    | ||   |||||||| |||| ||||||||| |    ||||| ||||  ||  ||||||| || || ||||||||||| ||||||||||| ||||| |||||||||||||      | || 
-----------------gtgcgcctccttcctccttctctctcgctcgtt--tgttggtgtggctggatctcgctc-----acgg--------gttcttggggtggtgaattttttttcgcagCAAGGTGGTGCGCACCTCGATCGCGCGCGTGCTGACGGTGATCTCGCAGAAGCAGAAGGCGGCGCTGAGGGAGGCGTACAAGAAGAAGAGCCTGCTCCCG

upper sequence: GLYMA13G19650.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g30050.1 (Oryza sativa), 3'ss of exon 2
gtaccaactcacttccaacattttctcagtgtttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC
                   |    ||  | | | |    ||  | | ||| |      | |  | |   |     ||||||  ||             || |||    | | |  |||||||| ||||||||| |    ||||| |||| |||  ||||||| || || ||||||||||  ||||||||| | ||||| |||||||||||||      | |||
-----------------gtacgcgcttcgcgctcgcgc-tcgcgctcattctctcctctttctgtgtgcc----cttgtgattga-------------ttgaatc---tctgtggttttgcagCAAGGTGGTGCGCACGTCGATCGCGCGGGTGCTGACGGTGATCTCGCAGAAGCAGAGGGCGGCGCTGCGTGAGGCGTACAAGAAGAAGAGCCTCCTCCCC

upper sequence: GLYMA13G19650.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G010599_T02 (Zea mays), 3'ss of exon 2
gtaccaactcacttccaacattttctcagtg-tttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC
                      | ||   ||  ||    | |||  ||  |  | ||   || | ||  | || |     || |  |||  ||  | |  |   | ||||  | | ||  |||| ||| | ||| |    || || || |  ||  | || || || || |||||||||||  |||||||| | ||||| |||||||||||||||  | | || 
-----------------gtgcctgcttgatggctttgccgcccttcttcctcgt-ttgtcatactggctttgcatc----gagctgaaccgaatcgtggatccgtggtttcctctctt--gcagCAAGATCGTGCGCACCTCCATCGCTCGCGTGCTCACCGTCATCTCGCAGAAGCAGAAGTCGGCGCTGCGTGAGGCGTACAAGAAGAAGAAGCTTCTCCCG

upper sequence: GLYMA13G19650.1 (Glycine max), 3'ss of exon 1
lower sequence: AC206642.4_FGT001 (Zea mays), 3'ss of exon 2
gtaccaactcacttccaacattttctcagtgt-ttgtttgtcctgattattattattagtatgcgggaatcgcgtt-ttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC
                            |||  |||   |  ||     || ||  |  | |     | | || ||  |  | ||  |||  ||  | |  |   | ||||    | ||  |||| ||||| ||| |    || || ||||  ||  |||| || || || |||||||||||  |||||||| | ||||| |||||||||||||||    | || 
----------------------------gtgcgttgacggcgctcgcccttgttcctcttttatcaaactggctttgcttcggacttaacttaatcgtggatccgtggtttccactctt--gcagCAAGGTTGTGCGCACCTCCATCGCGCGCGTGCTGACCGTCATCTCGCAGAAGCAGAAGTCGGCGCTGCGTGAGGCGTACAAGAAGAAGAAGCTGCTCCCG

upper sequence: GLYMA13G19650.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G010599_T03 (Zea mays), 3'ss of exon 2
gtaccaactcacttccaacattttctcagtg-tttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC----
                      | ||   ||  ||    | |||  ||  |  | ||   || | ||  | || |     || |  |||  ||  | |  |   | ||||  | | ||  |||| ||| | ||| |    || || || |  ||  | || || || || |||||||||||  |||||||| | ||||| |||||||||||||||  | | ||     
-----------------gtgcctgcttgatggctttgccgcccttcttcctcgt-ttgtcatactggctttgcatc----gagctgaaccgaatcgtggatccgtggtttcctctctt--gcagcaagATCGTGCGCACCTCCATCGCTCGCGTGCTCACCGTCATCTCGCAGAAGCAGAAGTCGGCGCTGCGTGAGGCGTACAAGAAGAAGAAGCTTCTCCCGCTCG

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|10844155|gb|BF067487.1|BF067487
EST:     CTCCGCGTCGCCAAGGTTACCCGCGGCGCCCCAAACAAGCTCTCCAAAAT                         TAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAA
genomic: CTCCGCGTCGCCAAGGTTACCGGCGGCGCCCCAAACAAGCTCTCCAAAATgtaccaactc ... ttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAA
EST: gi|207816180|gb|GD786181.1|GD786181
EST:     CTCCGCGTCGCCAAGGTTACCGGCGGCGCCCCAAACAAGCTCTCCAAAAT                         TAAGGTGATGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAA
genomic: CTCCGCGTCGCCAAGGTTACCGGCGGCGCCCCAAACAAGCTCTCCAAAATgtaccaactc ... ttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC
                             ttttaat  putative branch site (score: 3)
                             ttttaattgttttttt  CT-rich tract
                             ttttaattgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaactcacttccaacattttctcagtgtttgtttgtcctgattattattattagtatgcgggaatcgcgttttgtgaacgaaacgaaacggcgttttaattgtttttttttttttgcagTAAGGTGGTGAGGCTATCGATAGCGCAGGTTTTGACGGTTATTTCCCAGAAGCAGAAAGCGGCGCTGAGAGAGGCTTACAAGAAGAAGAAGTATTTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT