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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC

Basic information

species Glycine max
transcript GLYMA08G44580.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 7
gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttct--ctttttga---aaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC
                        ||||   |  ||| |   | |  | || |    | ||| | ||||  |||  |||  |||    || |  | | | || |||     |     ||  |   |    |||| || ||||| ||||| |||||||||||||| |  |||||||||||||||||| | || || ||  | || ||||| ||  |  ||||||||||||| |
-----------------------gacatcagtgggtt-tggcattagaaataa----tcagattgtcatcctcttgcttgctgatatcaaattccctcgctaattttgttttc----ttctgtcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAGTGGCGCAATCTAGTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTC

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 8
gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC
                                         ||    || |   | ||       |||   | | |||||               || ||||       | ||||| || | || |||| || ||||||||||| ||||| || ||||| ||||| || |||||||||||||||| ||||||| |  | |||||    ||| ||||||||||||| |
----------------------------------------gtaagttacttactttttttcctcttcaccctatattttt-----tctttgaaagtaatttc----ccgagttttgaatgt-ttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC
|| |    ||  || |||       |  | |||  ||||  |  | ||| ||     ||     |||||  |  |  ||   ||  | |  |  | |||       |  || |||    ||    |||| || |||||||| |||||||| ||||| || | ||| || |||||||||||||||| ||||||| |  | ||||| || ||| | ||||| ||||| |
gtgtggttcc--ttcctaccctgctcgatactatattcttgt--tccac-tgttgtatagccaactcatgatagcagttgagaa--taaagtaaagagt---ggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 6
gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC
                       | | |   ||||    |  |        ||  || ||   |   ||||| | ||| |   | |   |    |||   |     |    |  || |||  |  ||||||| |||||||| || ||||| |||||||| ||||||||||| ||||||||||||| ||||||| | || || || || ||||||||||| ||||| |
----------------------ctccttggttaag---cagcaagttgagggaaactcaat--ttggattttgtatttgttgcatccatctcttataacctttttttattttggtgcattgttccagACCTTTGAGGAAGCTGACACAAAACATGATGGAAAGATTGACAAAGAAGAGTGGAGAAGCCTTGTTCTACGACACCCATCCCTTTTGAAGAATATGACTC

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|213597200|gb|DB981592.1|DB981592
EST:     AATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG                         ACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAG
genomic: AATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAGgttttacccc ... atttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAG
EST: gi|209710674|gb|BW671020.1|BW671020
EST:     AATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG                         ACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAG
genomic: AATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAGgttttacccc ... atttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAG
EST: gi|7234008|gb|AW569349.1|AW569349
EST:     AATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG                         ACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAG
genomic: AATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAGgttttacccc ... atttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC
           aactcac  putative branch site (score: 2)
                                              tttcttt  putative PPT
                      atagtttcaacattaa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttaccccattttctataacttacatttctaagttctaatagtgcacatgagtcttaagagtctcattttctctttttgaaaactcacatggatagtttcaacattaaattttggatttctttagACCTTCGAGGAAGCAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC