Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttattactatattgattaattttttttaatttaataaagataattgtaataaatgtagttgacacttccttgcttatgagtctttcacttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG

Basic information

species Glycine max
transcript GLYMA17G38220.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 4
----tgttattactatattgattaattttttttaatttaataaagataattgtaataaatgtagttgacacttccttgcttatgagtctttcacttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG
       ||  | | ||     |       | || ||| |||    || || |   |    ||||| |  |   | || | | ||||  |  | || |   |||||||||||  |||| || ||||| |||| |||  |||||||||||||||| || |||||  | || ||||||||||||||||| || || |||
ccttgactaacagtctaccttcttgaagaatgtattttcatatctgtatttatgggactattagtttatgc--acatgatgaggagtaat--atttctttccagGGAGATACATTAGACTATCTTGGCATCCCAGGATTTCACTTTGCTGGAAGCCAAGGAGTAATTGTCATTGCTATTTGCCAAGCCCTGCTGATG
















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|151404614|gb|EV274428.1|EV274428
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|209714193|gb|BW679522.1|BW679522
EST:     TCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|209716259|gb|BW657562.1|BW657562
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|120491987|gb|EH220154.1|EH220154
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|151395535|gb|EV265412.1|EV265412
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATC
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATC
EST: gi|120491971|gb|EH220138.1|EH220138
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|193615748|gb|FK561961.1|FK561961
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGACGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|209714192|gb|BW679521.1|BW679521
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCT
EST: gi|22539788|gb|BU089631.1|BU089631
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAC                         GGAGATACTCTAGATTACCTTGGTATGCAAG-TCGTCACTGTGGCTGGA
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTG-CTGGA
EST: gi|24136537|gb|BU927047.1|BU927047
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|31462175|gb|CD404203.1|CD404203
EST:     GCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: GCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|51337747|gb|CO981613.1|CO981613
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|22524231|gb|BU083042.1|BU083042
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|7283675|gb|AW596279.1|AW596279
EST:     GGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: GGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|192297292|gb|FG990626.1|FG990626
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATC
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATC
EST: gi|209703879|gb|BW667920.1|BW667920
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTG
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTG
EST: gi|31458047|gb|CD400075.1|CD400075
EST:     GGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: GGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|151404020|gb|EV273830.1|EV273830
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|120533754|gb|EH261887.1|EH261887
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|31466890|gb|CD408918.1|CD408918
EST:     TTCACTTTGTAGAACCAGTGTGTTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
EST: gi|13481342|gb|BG510685.1|BG510685
EST:     TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAG                         GGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT
genomic: TTCACTTTGTAGAACCAGTGTGGTGGCGTGTTGGATATTCAAAGCTCAAGgttattatgt ... ttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaataaatgtagttgacacttccttgcttatgagtctttcacttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG
             agttgac  putative branch site (score: 4)
                                     tctttcacttttc  putative PPT
     ataaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttattactatattgattaattttttttaatttaataaagataattgtaataaatgtagttgacacttccttgcttatgagtctttcacttttcaacagGGAGATACTCTAGATTACCTTGGTATCCAAGGTCTTCACTTTGCTGGAAGTCAGGGAGTGGTCGTGATTGCTATTTGCCAAGCACTCCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG