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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagttaatgcaatctctcaggtcatttcaataacttggtcttcctcaacag

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagtta--atgcaatctctcaggtcatttcaataacttggtcttc----ctcaacag----------------------------------------------------------------------
 || ||  | ||||| || ||||||||  | |||||||| ||||| || ||||||||||| || ||||| |||||||||||||||||  | ||||| |||||     ||   | |     |    |  ||||  | ||  || || | || |  || |  |   |  |    |  || ||||||  | | |    ||||  ||                                                                      
AGACACGCTACCTTCAGAATATGATTCACGGGTTAAGGCAATGGAGGTAGATGAAAAGCCTACAGAGGATTACAATGACATTGGTGGCCTTGAGAAACAGgtatttatttactttaaagatctaatgatgaaaacattagttaggatggtcaccattctgttgttatgtaagtagcagtaacttcatttccatatctcataagtgttcatcagttgctgtttgttcattgttatctgctctcttatgttctacttttatattgtctaatgcag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagct--ttggttcttgccttaa-tttattgaagccctt----gtttgggttagttaatgcaatctctc---aggtcatttcaataacttggtcttcctca-acag----------------------------------------------------------------------------
||| ||  |||| || |||||||||||  |||| ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||  | || ||||||||    |  ||  |   ||    || || | ||   |  ||      | |   || | |   | ||||||     |   | |  |  || |||     | |||  ||                                                                             
GGACACACTGCCATCAGAGTATGATTCACGAGTAAAGGCAATGGAGGTGGATGAAAAACCCACAGAGGACTACAATGATATTGGAGGTCTTGAAAAGCAGgtacattgcttaataaatgttgaaagttcagtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtga---gcttt---ggttcttgccttaatt----tattgaagcccttgtt-tgggttagtta--atgcaatctctcaggtcatttcaataacttggtcttcctcaacag
 ||||| |||||||| |||||||| ||  | |||||||| |||||||| ||||| || || || ||||| |||||||||||||| ||| | ||||| ||||| |   |||||   |      |  |||| |    |||     |   |||| ||| || ||||   ||||| |   |||   | |   ||   ||||| |  | ||    
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcag--taatatgatg-tttggtataacacag---

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagttaatgcaatctctcaggtcatttcaataacttggtcttcctcaacag---
 ||||| ||||| || ||||| |||||  |||| ||||| |||||||| ||||||||||| || || || || ||||||||||| ||  | || ||||||                                                                                                    
AGATACATTGCCATCAGAGTACGATTCACGAGTGAAGGCAATGGAAGTGGATGAAAAGCCCACTGAAGATTATAATGACATTGGGGGTCTTGAAAAGCAGnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagtt--aatgcaatctctcaggtcatttcaataacttggtcttcc---tcaacag
|||||| || ||||||||||||||||| ||||| || || ||||| || || ||||| || || || ||||||||||| || || ||| |||| || ||||  ||  ||| |   |  | |  || || |   || | ||||    ||  |    | |||| | | | ||   |  | |  | || | ||     | |||||
GGATACTTTACCTTCTGAGTATGATTCAAGAGTAAAAGCAATGGAGGTCGACGAAAAACCTACTGAAGACTACAATGATATAGGGGGACTAGAAAAACAGgctag--ttgatgactctcctgtttcat-gtttccttagtttttagtatctctggtacaatatttgatgttggtg-actctcctgtttttgtaattaaacag

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaa--gcccttgtttgggttagttaatgcaatctctcaggtcatttcaataacttggtcttcctcaacag
|||||||||||| || |||||||| ||||| ||||| |||||||| || |||||||| ||||| || || |||||||||||||| ||| |||||||||||||  | ||      |||  ||||| |  || |  | | ||| || |  |||| ||   |||   | || | |||||   |||                 
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcg--tagtgaaactaat---tgagtttatttctggaacag---------------

upper sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 4
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagttaatgcaatctctcaggtcatttcaat---aacttggtcttcct--caacag
 ||||| ||||| ||||||||||||||| |||| ||||| ||||| ||||||||||| ||||| || ||||||||||| || || ||  | ||||||||||  || ||   || |   | || ||||| ||||   |||||       | |  | | || | |  | |  ||||||    ||||||    |  |  ||||||
AGATACTTTGCCATCTGAGTATGATTCTCGAGTAAAGGCTATGGAGGTTGATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagtttcaattttgtgcatattttatggaagtggttgtt-------gcttgtccgattttt--gatactttcaactaaaacttgcctctaattacaacag

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|6915777|gb|AW397307.1|AW397307
EST:     ATGAAAAGCCCACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATT-GTTG
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTG
EST: gi|254339477|gb|GR848235.1|GR848235
EST:     ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
EST: gi|4313874|gb|AI460993.1|AI460993
EST:     ATGANAAGCCAACCGAGGACTACCATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATTAGT
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGT
EST: gi|209719376|gb|BW674456.1|BW674456
EST:     ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
EST: gi|120530681|gb|EH258814.1|EH258814
EST:     ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
EST: gi|254342561|gb|GR858723.1|GR858723
EST:     ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
EST: gi|7924448|gb|AW830474.1|AW830474
EST:     ATGAAAAGCCAACCGANGACTACAATGACATTGGTGGATTAGAGANGCAG                         ATTCAAGAATT
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATT
EST: gi|22525777|gb|BU084588.1|BU084588
EST:     ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAG                         ATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA
EST: gi|7042249|gb|AW472143.1|AW472143
EST:     ATGATAAGCCAACCGATGACTACAATGACATTGGTGGATTAGAGAAGCAT                         ATTCAAGAATGAGTTGAAGCTATTGTTTTGCCCATGACCCACAAAGAGCGA
genomic: ATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttg ... tcctcaacagATTCAAGAATTAGTTGAAGCTATTGTTTTGCCCATGACCCACAAGGAGCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaagcccttgtttgggttagttaatgcaatctctcaggtcatttcaataacttggtcttcctcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC