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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag

Basic information

species Glycine max
transcript GLYMA14G01290.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagca--ctgccttgact--ctaaattttggtaccttgcgatgataac-tgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag
 ||  | || |||| || |||||| ||||| ||||| || ||||| |||||||| ||||||||||| |||||||| || ||||||||||| ||||| ||||||        |  |||  || |||  | |||||||      ||    |  ||   | ||  | |   |||| | | |   |    ||  || ||   ||    | | 
CTCGAGGGCCTATGGAAACAACATTGGTGGTTACAAGAACGAGGGGTTTGTTGAAGTTCTTGCTGCGCAGCAGAGCCCAGAGAATCCTAACTGGTTTCAGgtatcttggttaatctgtattaacttgccaaatttt------ttatagtagtactgtattagtttgaattgactcggtaagt-ggtaatttttgtactatgcaggta-

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactc----taaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag
 ||  | || |||| || |||||| |  || ||||| ||||||||||| |||||||| ||||| || || |||||||| |||||||| || ||||| ||||||          |   |||||      | |||||    | | ||   |  ||  |  || ||      |   ||||  | |   | ||   |              
CTCGAGGGCCTATGGAAACAACATTGCCGGGTACAAGAATGAGGGATTCGTTGAGGTCCTTGCAGCACAACAGAGTCCAGAGAATCCCAACTGGTTTCAGgtatctttgtttatctgttgacatgtgatcaatttattcatcctggattattagttcatgctgataacaggagtgataatgtttgataccaagcacatct-------

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag
||| || |||||||| || ||||||||||| ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| || || ||||| |||||||   || |  ||| |      |    || |  ||       |   || |  ||   || ||| | ||  | || |  |    |   |   |  ||| || 
TTCCCGGGCTTATGCCAGTAACATGGGTGGGTACAAGAATGAAGGGTTTGTTGAAGTTCTTGCTGCTCAGCAGAGTCCTGAGAACCCCAACTGGTTTCAGgtaagaacatcg-tgcttcagtggtgtgcttggaaactcattttttggaattcctgcaatctcttcaattc-tattgtttctgtttgatttcaaaaattcca-

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S2_337V6.1 (Physcomitrella patens), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag
 ||||| || ||||| | |||| ||||  | || | ||||||||| ||||| ||| |||| ||||| |||||||||| ||| ||||| |||||||||||||||      |  ||   |      |  | | | |  | |||   |          |   |  ||  || |    | || | |  |  |     ||||  |   
GTCTCGAGCATATGCTACCAACTTGGGGAGTTATAGAAATGAGGGTTTTGTAGAGATTCTGGCTGCCCAGCAGAGTCATGACAATCCCAATTGGTTCCAGgtataatttgtcctttttctgtcatcgactctcgagctttgt--ttcctttctcagacatgtctgaatcttgattcttgagattcaggaccaaatcaaagat-

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaatt-----ttggtaccttgcgatgataactgttgttgtcccttgatttgatgttt-taacaaacttggtgtgatcattgcag------------------------------------------------------------------
 || || ||||| |||||||| ||||| || ||||| || || ||||| || || ||| | ||||| || || |||||||||||||| |||||||| |||||   |  |  | | | | |  | | | ||     ||   ||     ||   |     |||  || ||| ||  |    ||  ||||          ||  ||   ||                                                                   
GTCCCGAGCTTACGCAAGCAATATGGGGGGATACAAGAACGAAGGATTCGTGGAAGTTTTAGCTGCCCAACAAAGTCCTGAGAATCCCAATTGGTTTCAGgtgcag--attatttcttagcgtgtgagttgttgatttacactcaaagaaattggtgtttgcggtgcctggaacttgcattcgtaacgcgtaataactggccagaacacgttctgtaattgaaattcagtgatgatgtgattatgctcacaatgttgtaaactgttgtgattcag

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgta--atgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag---
 || || ||||| || || |||||||| || ||||| ||||| || || || |||||| | ||||| ||||||||||| ||||||||||||||||| ||||||  || || |||      | | ||  |||  |||    |||  |||    |||| |   | |  |||     |       |  || || |||  |||         
GTCCCGAGCTTACGCTAGTAACATGGGAGGGTACAAGAATGAAGGTTTCGTGGAGGTTTTGGCTGCCCAGCAGAGTCCCGAGAATCCTAATTGGTTTCAGgtatgatacctgcata----taattcacaatcgtgggtttttg-aatg--ggctgt-gcaattctctgagaatcttcccagtcttacctgatgtcctcacgctgagat

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ17026 (Selaginella moellendorffii), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag
 || || |||||| | || ||||||||   |||||| || || ||||| || |||||||| |||||||| || ||||| ||||||||||| ||||| ||||||||        ||   | |    |  ||||     || ||  |   | |||   ||||   |||                                     
ATCGCGAGCTTATTCCAGTAACATGGGAAACTACAAGAACGAAGGATTCGTGGAGGTTCTCGCTGCTCAACAAAGTCCCGAGAATCCTAACTGGTTTCAGgtaat--------tgttctcaa---agtttttaagttctcgcagttccagctgaaattgttttttgtag----------------------------------

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ16157 (Selaginella moellendorffii), 5'ss of exon 2
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag
 || || |||||| | || ||||||||   |||||| || || ||||| || |||||||| |||||||| || ||||| ||||||||||| ||||| ||||||||    |  || |   |  | ||| || | | |  |   | ||| | ||||| ||||                                           
ATCGCGAGCTTATTCCAGTAACATGGGAAACTACAAGAACGAAGGATTCGTGGAGGTTCTCGCTGCTCAACAAAGTCCCGAGAATCCTAACTGGTTTCAGgtaatt---gttct-caaagtttttaagttctcgcagttccagctga-agctgtttttgtag-----------------------------------------

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|15337832|gb|BI498488.1|BI498488
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGG
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGG
EST: gi|13478311|gb|BG507837.1|BG507837
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
EST: gi|120532534|gb|EH260667.1|EH260667
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
EST: gi|17022405|gb|BM093439.1|BM093439
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTAT
EST: gi|7796534|gb|AW781931.1|AW781931
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGAT
EST: gi|22521682|gb|BU080493.1|BU080493
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
EST: gi|209712745|gb|BW681599.1|BW681599
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
EST: gi|17400675|gb|BM177457.1|BM177457
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAA
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAA
EST: gi|23728291|gb|BU762193.1|BU762193
EST:     TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAG                         GGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT
genomic: TTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccag ... atcattgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTCGTGCTTATGCAAGCAACATGGGTGGCTACAAAAATGAGGGATTTGTTGAGGTTCTTGCTGCTCAGCAGAGTCCTGAGAATCCTAATTGGTTCCAGgtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT