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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgatgatgtctattagtgtgcaattatttctttttatgtgaatgcatatttttatctgcgatgttcattatttgacagatttaaattttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACTCTATCTGAGCAGTG

Basic information

species Glycine max
transcript GLYMA14G04890.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 10
tgctgatgatgtct-attagtgtg---caattatttctttttatgtgaatgcatatttttatctgcgatgttcattatttgacagatttaaattttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACTCTATCTGAGCAGTG
|||| || | |||| | ||| | ||| | | | | ||||| | | || |||| || || ||| |||| | || | || ||| | ||||||||||| || ||||||||||||||||||||||| ||||| || || || || ||||| |||||
-actgaacattcgggaatagtatatatcaagtttttgatgctttattgatgcaaaatggatactat--tgtttatctctt-acacattttgacgttgtttgtagTGTTCTAGTTCACAGTGGCGGAGTGCATGGTGGACATTATTATGCCTTTATAAGACCCACCCTTTCTGATCAGTG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------tgctgatgatgtctattagtgtgcaattatttctttttatgt----gaatgcatatttttatctgcgatgttcattat----ttgacagatttaaattttttcc--------acagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACTCTATCTGAGCAGTG
|| | | || || | | | |||| ||||| | | ||| | | || | || | || | | ||| | ||||| ||| || |||||||||||||||| || |||||||| ||||| || ||||||||||| || || || ||||| |||||
gtttggggcataatcattcgattctcgtgttaatgttttcctgatgttttatacatccctttttacttattaatttatttttttcttacagaaggtgtgccttgtgccaaaatttattgcatcgcctcaattgatattggcttttttttgttcgtggcagTGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTG
















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|51334822|gb|CO978688.1|CO978688
EST:     TTATCACCTGATGCTGATAGGAATGTCCGCAATCTTTACACACTTCATAG                         CGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTAT
genomic: TTATCACCTGATGCTGATAGGAATGTCCGCAATCTTTACACACTTCATAGgtaatgtagt ... ttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTAT
EST: gi|207769067|gb|GD741983.1|GD741983
EST:     TCACCTGATGCTGATAGGAATGTCCGCAATCTTTACACACTTCATAG                         CGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTAT
genomic: TCACCTGATGCTGATAGGAATGTCCGCAATCTTTACACACTTCATAGgtaatgtagt ... ttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTAT
EST: gi|254325768|gb|GR838649.1|GR838649
EST:     TTATCACCTGATGCTGATAGGAATGTCCGCAATCTTTACACACTTCATAG                         CGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTAT
genomic: TTATCACCTGATGCTGATAGGAATGTCCGCAATCTTTACACACTTCATAGgtaatgtagt ... ttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatatttttatctgcgatgttcattatttgacagatttaaattttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACTCTATCTGAGCAGTG
                           atttgac  putative branch site (score: 4)
 ttttttccac  putative PPT
 ttcattatttgacaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgatgatgtctattagtgtgcaattatttctttttatgtgaatgcatatttttatctgcgatgttcattatttgacagatttaaattttttccacagCGTTTTGGTTCACAGTGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACTCTATCTGAGCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
tgctgat
- - - - - - - - - gtgtgca
- - - - - - - - - - - - - - - - - - - - - gaatgca