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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctttctctctctctctctctctctttttcttctctgatttcctttcagatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG

Basic information

species Glycine max
transcript GLYMA11G34840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G439457_T02 (Zea mays), 3'ss of exon 2
gtcctttctctctctctctctctctctttttcttctctgatttcctttcagatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG
   | |  | |   |     |||||   |||  |      ||| |||||     | || || ||| | ||    |   | |  ||| | |  ||   |  || |||| |||||||| ||||| || ||||||||||| ||| | |||||||||||||| || || || ||||| |||   ||||| ||||| ||
---cctgatatgcttgatgatctctaagttttctaggaagtttgctttctctcattgcctttttc-ttaccatacaggcttatttagtattttgc-ctattgtagGTCAGTTTGAGTGCATTTGCATTCTTGTTCTCTGAGTTGGTTCAGTACAACCAGACTCAAGTTGACAACATTACTGAGCTGGAACGGAG

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 3'ss of exon 1
-gtcctttctctctctctctctctctctttttcttctc-tgatttcctttcagatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG
 |   ||  |||   |||   |   ||| ||| || |  | |||   ||||     ||   | ||| || | | || ||  |   |  | |||      || || |||| || |||| |||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| |  || |||||| ||||
gggttttgatcttcttcttctttgatctctttattgtgatcattcgatttcgagcatctgctgattggttagt-cgttttggaactgtacttg------tgttgtagGTGAGCTTGACCGCATTTGCTTTCTTATTCTCGGAGCTCGTTCAGTACAATCAAACCCAGGTTGACAATATAGCTGAACTTGAAAGAAG

upper sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 1
gtcctttctctct-ctctctctctctctttttcttctctgatttcctttcagatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG
 |   |  ||||  |  ||   |  |  ||| ||    |     |||||   || |||  || |    |   | | ||   |     | ||||| | | | | ||||| |||||||| ||||| || |||||||| ||||||||||| |||||||| ||| | |||||||| || ||||  ||  | ||| ||||
-ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttcg--ttctggagcgtatagttttgttaa--gaattgat-tttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG

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|151411948|gb|EV281759.1|EV281759
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTCCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|151396616|gb|EV266493.1|EV266493
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATT-GCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|151410774|gb|EV280589.1|EV280589
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|192320522|gb|FK011932.1|FK011932
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|298191865|gb|HO035947.1|HO035947
EST:     AGCAGTACATTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCACGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|13477866|gb|BG507568.1|BG507568
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|207756090|gb|GD730013.1|GD730013
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|151405191|gb|EV275005.1|EV275005
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|8286428|gb|BE023996.1|BE023996
EST:     GACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: GACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|192320523|gb|FK011933.1|FK011933
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|151412057|gb|EV281869.1|EV281869
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|42723157|gb|CK769056.1|CK769056
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
EST: gi|9987096|gb|BE661204.1|BE661204
EST:     AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAG                         GTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC
genomic: AGCAGTACAGTAACGTCCTCGACAAGCCCCTCACCAAGGGCAAGCAAGAGgtcctttctc ... gttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG
                                 ttaatttgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctttctctctctctctctctctctttttcttctctgatttcctttcagatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT