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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactgcaaaatgaatattattaaaacacaaggattaaaccaca...

Basic information

species Glycine max
transcript GLYMA03G39500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagattgtttcttgtcttcaatagtttt--ttttgaaactgcaaaatgaatattatt---aaaacacaaggattaaaccaca
||| || || || |||||||| || || |||||| | || |||||| | ||||| ||||||||||||||||||||||| || ||||| || ||  |||| || | ||     | ||  |  ||    |  |   ||  || | | | |||   |  |   | || |  |      |||||    |||   ||  | |  |  |  
AATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCACAAGACAAgtaagaa---caaaaacctggtttccctattcctttagctcctagattttacatcatatgaatggacgacttcctttattcatgaaatggaaaaaattgatta--

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactgcaaaatgaatatt--attaaaacacaaggattaaaccaca-
||| || || || ||||| || ||||| |||||| | ||||| ||||| || || ||||||||||||||||| |||||  | |||||||| ||  |||| || |   | || |    || |     ||    |    |  | |  | |  ||    || | |  || |   || |  ||  | |     |      |  | | 
AATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCACAAGACAAgtaagtcaacttac---ttgacggtcatctgctacctttctgatgaatcattaaacaagcagtcaagttcttacttgatctatattttggagactcatgataa

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactgcaaaatgaatattattaaaacacaagga--ttaaaccaca
||| || || || ||||| || |||||||||||| | ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||| ||  |||| || |  || ||   | |  ||||    | |     | |   |  ||   | | || |   ||   |   |   | | | || |||  | |  || ||     
AATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCACCAGACAAgtaagtaaacttgca-tgaaatttctgtagccaactatgaaccttatcatatattaactttgtccatcaatggtcaatcaagcacttgaactttgaattga-

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatt--taattaagattgtttcttgt-cttcaatagttttttttgaaactgcaaaatgaatattattaaaacacaaggattaaaccaca
||| || || || |||||||| || || |||||| | ||||||||| | ||||| ||||||||||||||||||||||| || ||||| || ||  |||| ||||  || ||| |   |  | || | | |  | |||| | ||    |  |||||| ||       | | || ||    |  |    | |    |    |   
AATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCACAAGACAAgtgagcaatctgttctctgctcatcagggtcatgtcttttgctgttctttttttttgtgtgttcatatactgtatgcattccactttctaaatctctgac---

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgaca-----aagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactgcaaaatgaatattattaaaacacaaggattaaaccaca-
 || |||||||||||||| || || ||||||||| | || |||||||||||||| ||| |||||||||||||||||||| | || || ||||| || ||||||| |     || |  ||  ||||  || | ||  | | | |  ||    ||||    |   |   |  |   |||| | ||      |      |  ||  || 
GATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTACACGGCAGgtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgtt-ttcgttatgtggactgcag

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagat-----tgtttcttgtcttcaa--tagttttttttgaaactgcaaaatgaatattattaaaacacaaggattaaaccaca
||| || ||||| ||||| ||||| ||||||||| | || |||||||||||||| || ||||| ||||||||||||||  | || |||||||| || |||||     |||  ||  | | ||||| ||     |  || |  | | |||  |||  ||  ||| | | | |||  |||| ||   |  ||     ||  |||     
AATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc--attttctcattaacatacatgtacttgtcttttacaaggtagagttaattggagcagtaaatggaatttt-cgaggacctgcagagcaaaa----

upper sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 3
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactg-caaaatgaatattattaaaa-cacaaggattaaaccaca-----------------
  | ||||||||||||||||| ||||| |||||| | ||  ||||| | ||||| ||||||| |||||| ||||| ||  | |||||||| || || || ||    ||| | |||     ||| |||||   ||| |   | |    ||     ||  |||| ||| |||||| | ||| | | ||    |     ||  ||                 
CGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCACACGTCAAgt----aagtt-atatccacattgagatt--ctctggcagtgacgttttccacatgtgactgtcaatatgaatttaatttatatcatgttgcactgacatcatttttttgtgtgtacag

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|209727631|gb|BW663793.1|BW663793
EST:     ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAG                         ACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
genomic: ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagc ... ttgactgtagACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
EST: gi|23727048|gb|BU761539.1|BU761539
EST:     ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAG                         ACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
genomic: ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagc ... ttgactgtagACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
EST: gi|209718165|gb|BW657811.1|BW657811
EST:     ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAG                         ACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
genomic: ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagc ... ttgactgtagACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
EST: gi|298168340|gb|HO014515.1|HO014515
EST:     ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAG                         ACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
genomic: ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagc ... ttgactgtagACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
EST: gi|17400340|gb|BM177122.1|BM177122
EST:     ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAG                         ACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT
genomic: ACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagc ... ttgactgtagACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTACTCGACAGgtgacaaagctgataatttaattaagattgtttcttgtcttcaatagttttttttgaaactgcaaaatgaatattattaaaacacaaggattaaaccaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA