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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactgactcacgcattttgggaaatttattatttattatttttgttttgtatctgcaactttagtacttatatatagcgagcctgttttcacatca...

Basic information

species Glycine max
transcript GLYMA12G17950.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 6
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactgactcacgcattttgggaaatttattatttattattt--ttgttttgtatctgcaactttagtacttatatatagcgagcctgttttcacatca
 |||||  | || || ||| ||||||| |||||  | ||||| || || ||||||||||| ||||||||||| || |  |||||||| || ||||||||||||  |   |   |  |  |||   | || |  | |  | |      || |  || |   || || ||   ||    |      |       ||| |||   
GTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCTGGTTCATCAGCAAAGGATGTTGCTAAACAGCTCAAGgtaaaataaaacaaaactattttctatatctggtctggaatgcagaattatcatgcaagagctacctttaaaccaccaacctttg----caatttaacag--

upper sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 5
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactgactc-acgcattttgggaaatttattatttattatttttgttttgtatctgcaactttagtacttatatatagcgagcctgttttcacatca
 || ||  | || || ||| ||||||| || ||  ||||||| ||||| ||||||||||| ||||||||||| || |  |||||||| |||||||||||||||  |    ||   | ||| ||   |  |  | |  |     | || | |||     |  |    |   |      | |  | |||| |     |||  |
GTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacagctttgcacatctttttatgtaaaattctgggcctgttcggtttcagcgtaaagtgctgcgaagctgctgttac-agccagcagctacagta

upper sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G130987_T04 (Zea mays), 5'ss of exon 5
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtatt-actgactcacgcattttgggaaatttattatttattatttttgttttgtatctgcaactttagtacttatatatagcgagcctgttttcacatca
 || ||  | || || ||| |||||||||||||  ||||||| || || ||||||||||| || |||||||| || |  |||||||| |||||||||||||||   ||  |   || ||| ||   |  |  | | ||  |  | ||||   |     |  | ||   |    ||     ||| |   |  | |   |   
GTTTTATGTGGTCTTCATGCTGTCAGCCTGTGCTCTGTTCTCAAAGACATGGATTGAAGTTTCCGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacggacaaatatacacatctttttatgtaaaattttggtcctgtttggcattggcataaagctgctggctgtaccagcagctacagtactctgttagg-

upper sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactgact-cacgcattttgggaaatttattattta--ttatttttgttttg--tatctgcaactttagtacttatatatagcgagcctgttttcacatca
 |||||  | || |||||| |||||||||||||  | ||||| || || ||||||||||| ||||||||||| || |  || ||||| |||||||| ||||||  ||    | || ||   |    |    ||| ||  |      |   ||| ||  | || |   || |  ||||| | |||    |  |   |||  ||   
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagtatcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatga--attcaaatttgcca---

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|20812894|gb|BQ297372.1|BQ297372
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
EST: gi|9900546|gb|BE609514.1|BE609514
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
EST: gi|17022954|gb|BM093988.1|BM093988
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
EST: gi|5342399|gb|AI794683.1|AI794683
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCATAGCAGTTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
EST: gi|5058135|gb|AI736611.1|AI736611
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGCAGTCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
EST: gi|5126396|gb|AI748132.1|AI748132
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
EST: gi|209703728|gb|BW670691.1|BW670691
EST:     GGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA
genomic: GGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactga ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAGTCAAACTTGCAGAAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactgactcacgcattttgggaaatttattatttattatttttgttttgtatctgcaactttagtacttatatatagcgagcctgttttcacatca

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA