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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatattatatgcactattattactcaagaagataaaatatcatgttatgttagaggctagagttagtgatggtttgtttgttgtggtttcttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA

Basic information

species Glycine max
transcript GLYMA16G04740.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04740.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07670.t01 (Vitis vinifera), 3'ss of exon 1
aaata-ttatatgcactattattactcaagaagataaaatatcatgttatgttagaggctagagtta-gtgatggtttg---tttgttgt--ggtttcttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA
   |  || |||  ||     | | |||   | |     |||||  | ||   | |    | | ||   | |   ||||   || ||| |  | | | | |   ||| ||| ||    ||||| ||||| || |||||||| |||||||||||||| || |||||||| |||||   ||| || ||||| || ||||| ||||| ||
gtttgcttctatatacctacctcattcatatataatccttatcaattaattaaaaataaaatacttgtattaaaatttgaagttggttttccgatctatgtctgcagGTAAAGCTGTTTTTGGCGAGAAGGAGTGGTATTTTTTCAGTCCTAGAGATCGCAAGTACCCCAATGGACTAAGACCCAACAGAGCTGCTGCGTCAGGCTA

upper sequence: GLYMA16G04740.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S140_93V6.1 (Physcomitrella patens), 3'ss of exon 1
-aaatattatatgcact-attattactcaagaagataaaatatcatgttatgttagaggctagagttagtgatggtttgtttgttgtggtttcttttat-cagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA
 ||   |       | | |     | | |   |  |||| |    |||     |      || |   |  || |||| |  | |  |     ||||  | |||  || || |  || || |||| |||||||||||||||||| ||  ||||| |||||||||||||||| || || || ||| | |||||||| || |||||
taagcttctcgcaaattgaacggaagttagttatttaaacttctgtgtccatgtgatcattaaa--caccga-ggttggagtataattaaaactttgctgcagGAAAAGCAATATTCGGAGAGAGAGAATGGTATTTCTTCAGCCCACGAGACAGAAAGTACCCAAATGGAGCCAGACCCAACCGAGCAGCTGCCTCTGGGTA

upper sequence: GLYMA16G04740.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S164_33V6.1 (Physcomitrella patens), 3'ss of exon 1
--aaatattatatgcactattattactcaagaagataaaatatcatgttatgttagaggctagagttagtgatggtttgt-ttgttgtggtttcttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA
  |     | | |||  ||||  |    |    ||    |     | || | ||  ||   | | || |  | | ||  | ||| | || | |    |  |||  ||||| |  || || ||   ||| |||||||| |||||||| || ||||| |||||||||||||| ||  | || ||| |||| || |||||||| | 
ccaggcggtgt-tgcgatatttctgggtagattgagtttaagatgtatt-tattgtagcacatacttcgataagattaatgttggtttgctctgacatg-cagGGAAGGCAATTTTAGGAGAAGGAGAGTGGTATTTTTTCAGTCCAAGGGACCGGAAGTACCCAAATGGGGCTCGACCCAACCGGGCTGCAGCTTCAGGATT

upper sequence: GLYMA16G04740.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
aaatattatatgcactattattactcaagaagataaaatatc--atgttatgttagaggctagagttagtgatggtttgtttgttgtggtttcttttat-cagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA
 | ||| || | ||| | | | |    ||    |||| ||||  |  | | | |  ||     |  || ||| | ||||  |    ||   | |||  | |||  || || |  || || ||||  |||||||||||||| |||||||||||  |||||||||| ||||| || ||||| ||||| || || |||||||||||
tagtatcatct-cacaaat-tgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatactga-gctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA

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|192302989|gb|FG997005.1|FG997005
EST:     CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAG                         CTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
genomic: CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAGgtttgcctct ... cttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
EST: gi|13481328|gb|BG510671.1|BG510671
EST:     CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAG                         CTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
genomic: CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAGgtttgcctct ... cttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
EST: gi|6069768|gb|AW099384.1|AW099384
EST:     CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAG                         CTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
genomic: CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAGgtttgcctct ... cttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
EST: gi|17402168|gb|BM178950.1|BM178950
EST:     CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAG                         CTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
genomic: CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAGgtttgcctct ... cttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
EST: gi|17402181|gb|BM178963.1|BM178963
EST:     CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAG                         CTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC
genomic: CATTATTGCTGAGGTTGATATCTACAAGTTAGATCCATGGGACTTACCAGgtttgcctct ... cttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgttagaggctagagttagtgatggtttgtttgttgtggtttcttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA
                                          tttcttttatc  CT-rich tract
                                          tttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatattatatgcactattattactcaagaagataaaatatcatgttatgttagaggctagagttagtgatggtttgtttgttgtggtttcttttatcagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - tatgcac
- - - - - - - - - - - - - - -aagataaa
- - - - - - - - - - - - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgtgg