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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattccctttgtgctgtttgacttgcaattgactgaggggtggggattgacttttagatgtagtaatttttgtgacatcttgtgattcattggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG

Basic information

species Glycine max
transcript GLYMA11G11510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 3'ss of exon 2
caattccctttgtgctgtttgacttgcaatt--gactga-ggggtggggattgacttttagatgtagtaatttttgtgacatcttgtgattcattggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG
   ||    |  |  | |   ||||| | ||   | ||| |||||     |||  ||    ||  | |  ||||  |  ||| | |    | |   |   ||||| || ||||||||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| |
-tgtttgtgtatttttttccaacttgaagtttgaattgatggggttacctttgtattgatcatcaacttgttttctt--catttggaatgtgacctggagcagGATTATGTGCCAACTGTATTTGACAATTTCAGTGCAAATGTTGTGGTGGATGGGAGCACTGTTAATCTAGGGTTGTGGGATACTGCAG

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 2
--caattccctttgtgctgtttgacttgcaattgactgaggggtggggattgacttttagatgtagtaatttttgtgacatcttgtgattcattggct-acagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG
  |      |   | | ||| |     |   |   |       |   |  |  ||  |   |  |   ||||||    || |   | |||  | |  |  ||||| ||||| ||||| || |||||||||||||| ||||||||||| || ||||||| ||| || ||||| || || |||||||| || |
ggcgtactgcaaggagatgtgttgtgcgatgtctcccattcactaaagtct--ctggtcccttcaacgatttttaaagca-cagataattggtcgttttgcagGATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAG

upper sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ04304 (Selaginella moellendorffii), 3'ss of exon 1
caattccctttgtgctgtttgacttgcaattgactgaggggtggggattgacttttagatgtagtaatttttgtgacatcttgtgattcattggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG
                                        ||| |  ||    ||    |    |     || | ||     |||| |   ||  | |||||||||||||| || |||||||| || || ||||| ||||| || |||||||| | |||||||||| | ||  | ||||| || ||||
----------------------------------------gtgagattttttcttctctttagatgggaattctaac----cgtgaatgtctgattccagGACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG

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|7589435|gb|AW705209.1|AW705209
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|298169211|gb|HO020571.1|HO020571
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|298197330|gb|HO044809.1|HO044809
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGC-AATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|298171990|gb|HO021582.1|HO021582
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|208187432|gb|GD984356.1|GD984356
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTC
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTC
EST: gi|16996922|gb|BM086294.1|BM086294
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|5760314|gb|AI965741.1|AI965741
EST:     GCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: GCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|151394170|gb|EV264041.1|EV264041
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|19346953|gb|BM891833.1|BM891833
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|298177328|gb|HO027109.1|HO027109
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTCGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|26058249|gb|CA801163.1|CA801163
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|5342846|gb|AI795130.1|AI795130
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGCTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|23725796|gb|BU760863.1|BU760863
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|298182534|gb|HO031269.1|HO031269
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|192329017|gb|FK021091.1|FK021091
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|192297529|gb|FG989535.1|FG989535
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
EST: gi|7589250|gb|AW705028.1|AW705028
EST:     TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACG                         GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT
genomic: TTGGCAAGACTTGCATGCTCATCTCCTACACCAGCAACACTTTTCCTACGgtcagtgcta ... ttggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgacttttagatgtagtaatttttgtgacatcttgtgattcattggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG
 gattgac  putative branch site (score: 3)
             atgtagtaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattccctttgtgctgtttgacttgcaattgactgaggggtggggattgacttttagatgtagtaatttttgtgacatcttgtgattcattggctacagGACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - -ccctttg
- - - - - - tgctgtt
- - - - - - - - - - - cttgcaa
- - - - - - - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - gggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgtg