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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatcttgtaattaaagggttgggcgtgtttgtaggttgaaataatagtttatcttataaatctttatgttcttttctcacctttcttatgtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCTCCTCCTTATCGTGGGCGTGAGGAGGTT

Basic information

species Glycine max
transcript GLYMA14G17930.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G17930.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 4
ctatcttgtaattaaaggg-ttgggcgtgtttgtaggttgaaataatagtttatcttataaatctt-tatgttcttt-tctcacctttctta----tgtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCTCCTCCTTATCGTGGGCGTGAGGAGGTT
         | |||  ||   | |||     ||  | ||     |||  || |  | || || ||| | |  |  |  ||| |    ||||     | ||  |  |||||||||||||| || ||||| ||||| || | |||||||||||| |||||||| || ||||| |||||||| ||    |||||||| ||||||||  | 
-------aaagttatgggaacttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG
















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|58025100|gb|CX711841.1|CX711841
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|298170870|gb|HO015846.1|HO015846
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGCAGGAGCCCAAGTTATGGGCGAAG                         ---T--C---C-TCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|213589771|gb|DB969592.1|DB969592
EST:     CGTAGCCGTAGTCCACCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCGCCGTAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|13790205|gb|BG652796.1|BG652796
EST:     CGTANCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|254321482|gb|GR824799.1|GR824799
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGC----                         --G--A-AGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|192324562|gb|FK016453.1|FK016453
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|151395696|gb|EV265573.1|EV265573
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAAGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|298185492|gb|HO030705.1|HO030705
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|7285723|gb|AW598210.1|AW598210
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTATGCACCGCAGATTGTCATCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|9983911|gb|BE658019.1|BE658019
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|192295485|gb|FG987099.1|FG987099
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|21675883|gb|BQ628234.1|BQ628234
EST:     AGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: AGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|8669525|gb|BE190632.1|BE190632
EST:     CGGAGCCGTAGTCCGCGCAGATTCCGTAGGAGCCCAAGTTATGGGCGAGG                         GAGTTACAGTCCTCGTGGGCGG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGG
EST: gi|298198145|gb|HO039684.1|HO039684
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCA
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCA
EST: gi|192300160|gb|FG989282.1|FG989282
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|298178379|gb|HO024114.1|HO024114
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAATTATGGGCGAAG                         ---T--C---C-TCGTGGGCGGTCCCCTAAGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|7591104|gb|AW706844.1|AW706844
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAAGAGCCCAAGTTTTGGGCCAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCATAAGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|298179203|gb|HO027674.1|HO027674
EST:     CGTAGCCGTAGTCCACCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCGCCGTAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
EST: gi|298165150|gb|HO011199.1|HO011199
EST:     CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAG                         GAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG
genomic: CGTAGCCGTAGTCCGCCCAGATTCCGTAGGAGCCCAAGTTATGGGCGAAGgtcagattgc ... gtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttatcttataaatctttatgttcttttctcacctttcttatgtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCTCCTCCTTATCGTGGGCGTGAGGAGGTT
                             ttctcac  putative branch site (score: 2)
                        ttcttttctcaccttt  CT-rich tract
         ttataaatctttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatcttgtaattaaagggttgggcgtgtttgtaggttgaaataatagtttatcttataaatctttatgttcttttctcacctttcttatgtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCTCCTCCTTATCGTGGGCGTGAGGAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG