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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgctactttagttgcacaataatgccattagcatgtcagcagccattattatagggagcacatgtgattctttgtgtcccttttt...

Basic information

species Glycine max
transcript GLYMA07G00350.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 14
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagt-tactgcttatgctactttagttgcacaataatgccattagcatgtcagcagccattat-tatagggagcacatgtgattctttgtgtcccttttt
| || |||||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| || |||||| ||||||| || ||  | ||||| ||||||||||| |  |   | |  | || || ||    |||  ||   |  |  |     |    | ||| |  |   |   |||   |   | |||  |  | || 
CTGCTGGTGGTGCCTGGGATAATGCTAAGAAGTACATCGAGACTGGCGCTCTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttttatcttttatgctctacttttcaaattctgttttgggggttgtttctaggactatgttcacacatttcat-caaaaatatgtagcaatatt-

upper sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 6
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact--gcttatgctactttagttgcacaataatgccattagcatgtcagcagccattattatagggagcacatgtgattctttgtgtcccttttt--------
| || || || ||||||||||||||||||||||||||||||||||| |||||||| |||||||| || ||| | ||||| || ||  | ||||| || ||||||||| ||  |||| || |    | ||  | |  | || |  |  |   |  || | | |   ||     |||   ||    ||| ||| | |               
CTGCTGGCGGCGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGCGCTCTTGGTGGCAAGGGCAGCGAGTCCCACAAGGCTGCGGTTACTGGCGACACgtaagtttctcagcttttggtgtcctggtgac-cttttatactttggg---gctagaatctagagtt-----gagtttatactgttcgttg-gccaagacagagcaaaga

upper sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G075900_T01 (Zea mays), 5'ss of exon 14
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact-gcttatgcta-ctttagttgcacaataatgccattagcatgtcagcagccattattatagggagcacatgtgattctttgtgtcccttttt
| || || || ||||||||||||||||||||||||||||||||||| || ||||| ||||| || |||||| | || || || ||  | || || || ||||||||| || | |||||||  | || ||  |  ||| |      ||   ||     ||  ||| ||     |||   ||    ||  |   |     |   
CTGCTGGCGGCGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGTGCCCTTGGTGGCAAAGGCAGTGAGTCCCATAAGGCTGCGGTTACAGGCGACACgtaagtttctagtttatgctctccttcgtgtcctaatgacttgtatactttggggctag--attcttgagctgagtttatactgttgatcaagcagagtaaa

upper sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 14
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgctactttagttgcacaataatgccattagcatgtcagcagccattattatagggagcacatgtgattctttgtgtcccttttt
| || || ||||| ||||| ||||||||||| ||||| ||||| || || ||||| ||||| |||||||| ||||||||||||||  | ||||| |||||||||||   |  |  | |||||| |          || |  ||   | ||    |      |  | |||    ||  ||  | |  | |           
CGGCGGGAGGTGCTTGGGACAATGCAAAGAAATACATAGAGACCGGGGCACTTGGGGGCAAAGGAAGTGAAGCTCACAAAGCAGCTGTGACTGGTGATACgtaagta--ttttcgttctacttcaacactcattcaaagttatattcctgaatacgatttctcat-tagaattcatctgaaaattgtag-----------

upper sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 15
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgctactttagttgcacaataatgccattagcatgtcagcagccattat-tatagggagcacatgtgattctttgtgtcccttttt----------------------------
||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| |||||||| ||||||||  | |||||||| ||  ||||||| ||||||||||  |    | ||  | |||  | | | |          ||    | |||   | ||||   | |       | |  | | ||    ||||   |  |                            
CAGCAGGAGGTGCTTGGGACAATGCAAAGAAATACATTGAGACTGGAGCTCTAGGAGGCAAAGGAAGTGATTCCCACAAAGCTGCAGTAACTGGTGATACgtaagcaatctttcattttccttgtgcttcccttcttcttagttcctttctcattggtcatttccttttacttataaagtttagtcgaactgtcttctaatgagaaatcgttattctgaaaatggcaag

upper sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 14
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgctactttagttgcacaataatgccattagcatgtcagcagccattattatagggagcacatgtgattctttgtgtcccttttt--
|||| |||||||||||||| |||||||||||||| || ||||| || || |||||||||||||||||||| || |||||||| ||  | || ||||| ||||||||  |   |  ||||   |  |  | |    ||||  |||      ||  |     ||| |  | ||  |    | |  | || |      ||||   
CAGCTGGTGGTGCCTGGGACAATGCAAAGAAGTATATAGAGACGGGCGCGCTTGGAGGCAAGGGAAGTGATGCCCACAAAGCTGCAGTTACCGGAGACACgtaagtctc-attcctgcttactggggggtagtcaaatga-atttcttgctcctcgtttgttaatccaagggtctatagcggctgttgggtaatgttttcca

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|193374597|gb|FK341551.1|FK341551
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACCGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTTAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
EST: gi|58016814|gb|CX703556.1|CX703556
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
EST: gi|192305808|gb|FG995736.1|FG995736
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
EST: gi|57575699|gb|CX548674.1|CX548674
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
EST: gi|14259734|gb|BG882642.1|BG882642
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
EST: gi|58018271|gb|CX705013.1|CX705013
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
EST: gi|58015021|gb|CX701763.1|CX701763
EST:     CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATAC                         AGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT
genomic: CTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttact ... aatttggcagAGTGGGAGACCCATTCAAAGACACAGCTGGGCCTTCAATCCATGTCCTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCAGGTGGTGCCTGGGATAATGCAAAGAAGTACATTGAGACTGGAGCTCTTGGAGGCAAGGGAAGTGAGGCTCACAAAGCAGCCATAACTGGAGATACgtaagttactgcttatgctactttagttgcacaataatgccattagcatgtcagcagccattattatagggagcacatgtgattctttgtgtcccttttt

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT