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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcctatgtttagtatattgtcaaaaatgttgtcttgagggttttgtttttttatttatggcatgttcttatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT

Basic information

species Glycine max
transcript GLYMA18G05730.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
ggcctatgtttagtatattgtcaaaaatgttgtcttgagggttttgtttttttatttatggcatgttct-tatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT-
  |  |  | |  |  |   |    | | |||      |   | | ||  |  | |      ||    | | |  | ||||  ||  | |||   |||| |||| |||||||||||||| || || ||||| ||||| || |||||||| ||  |||| || ||||||||||| || ||||| || ||||||||||||||| 
--ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 1
--ggcctatgtttagtatattgtcaa---aaatgttgtcttgagggttttgtttttttatttatggcatgttcttatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT-
       ||||||   || || | |    |||     |  | |  | || |  || |  |    |        | ||    ||||  ||||  |    ||| |||||| ||||||||||||||||| ||||| |||||||||||||| ||||| ||| ||||  | || |||||||| || |||||||| |||||||| |||||| 
tatttgaatgtttgccatctttttattgtaaacacatttctaaatggttggggttctggtcagagtttgaaattcatggtttttt--tgtacct----tttattagGATATTGGAGGATGTGATATTCAGAAGCAGGAAATCCGTGAAGCTGTTGAGTTACCTTTGACTCATCATGAGCTGTACAAACAGATTGGTATAGATCCTC

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 1
ggcctatgtttagtatattgtcaaaaatgttgtcttgagggttttgtt-tttttatttatggcatgttcttatccccttttcatgt-atttgatattt--tttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT-
     | |  | ||  ||   ||  ||| |  | ||      ||||   || |||    ||   | || | || |  |  |  |||    || |  |   |  |||| ||||| ||||| ||||| |||||||| |||||| | || ||||||||||| || ||||||||||| ||  |||| || || ||||||||||| ||  
-----aaggcttgttcatctgcatgaatctgttgttataatgtttgcaattcttacgagtgcagttttttaatactttcatattgtcgaatggtggtggatgcagGATATTGGTGGATGCGATATTCAGAAACAAGAAATCAGGGAAGCTGTGGAGCTTCCACTTACACATCACGAGTTATATAAGCAGATTGGTATTGACCCAC

upper sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 1
----ggcctatgtttagtatattgtcaaaaat--gttgtcttgagggttttgtttttttatttatggcatgttcttatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT-
         || |    ||||  || |  ||   | ||||||       |||||    | | ||||   |||||  | |     ||| |||   |||     |  |||| ||||| |||||||||||||| ||||| || ||  | ||||| |||||||| || ||||||||||||||||||||||| || ||||| || || ||  
agaaaaatgatttccgttatagggttacgaagcagatgtcttagtttaattgttcccatttatatgcattgttcaaagcga---ttcgtgttcgtgag----tgcagGATATTGGTGGATGTGATATACAAAAACAAGAGATTAGAGAGGCCGTGGAGCTTCCACTTACACATCATGAACTATACAAGCAGATTGGCATCGACCCAC

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|5607016|gb|AI901114.1|AI901114
EST:     TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAA                         TGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGA
genomic: TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAtgtcagtttc ... atattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGA
EST: gi|23050438|gb|BU577002.1|BU577002
EST:     TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAA                         TGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGA
genomic: TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAtgtcagtttc ... atattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGA
EST: gi|5508931|gb|AI855489.1|AI855489
EST:     TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAA                         TGACATTGGAGGATGTGATATACAGAAAACAGGAAATCCGTGAGGCTGTGG
genomic: TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAtgtcagtttc ... atattttttaGGACATTGGAGGATGTGATATACAG-AAACAGGAAATCCGTGAGGCTGTGG
EST: gi|10847367|gb|BF071532.1|BF071532
EST:     TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAA                         TGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGA
genomic: TCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAtgtcagtttc ... atattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttttatttatggcatgttcttatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT
                                        atttgat  putative branch site (score: 5)
                                              tatttttt  CT-rich tract
                               ttttcatgtatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcctatgtttagtatattgtcaaaaatgttgtcttgagggttttgtttttttatttatggcatgttcttatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT

- cctatgt
- - - - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - -ggttttg