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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT

Basic information

species Glycine max
transcript GLYMA19G30540.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT
|| |||   ||  | |||  | | |  |  ||    |  || |    |  ||||  | || |       |  |  |||      |   |  ||       |||| |||||||| ||||| ||||||||||| |||||||| ||||  || || || ||| | || || || || || ||||| || ||  ||||||| ||| 
gtgagc---tgcttaatcactgtta--tgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

upper sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaa----attgaaactttggactttgtttgtt--tagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT
                         ||    |||   ||| |  |   ||     || |    |  | | ||||||     | | |        | ||      ||| ||  | ||   ||  ||| |   ||||| |||| || || |||||||||||||| |||||||| |||||||| || || ||  | || ||||| || || |||||||||||||||||||||||| 
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
-gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT
   || | |  ||    | ||||||| | | |    || | | |  | | | | |   | | |  | || |     ||   ||    |   |    | |  ||||||| ||||| |||||    || ||||| |||||||| ||  |||| || || |||||||| ||||| |||||||||||||| |||||||| || ||  
aaatatc-tccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggc--ttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

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|208076991|gb|GD877782.1|GD877782
EST:     TGAAACCTGTCACAGGTGTCAGCCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCATCATCTGAA
genomic: TGAAACCTGTCACAGGTGTCAGCCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAA
EST: gi|208162324|gb|GD963097.1|GD963097
EST:     GAAACCTGTTCACAGGTGTCAGCCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCATCATCTGAA
genomic: GAAACCTG-TCACAGGTGTCAGCCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAA
EST: gi|58021832|gb|CX708573.1|CX708573
EST:     GTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAA
genomic: GTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT
                                         ctttgttt  CT-rich tract
                      taaaaattgaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA