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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGTGCGTCTCCGATGAAATCCAACACAACGTCGTCGTTTTGGCCGACTACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtacccttttgcgatttctctactgcctccttcttcaattactcattcgtctgtttgcttccttgatttgcgtgttgacggatttgttttctcctggatt...

Basic information

species Glycine max
transcript GLYMA08G13470.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G57620.1 (Arabidopsis thaliana), 5'ss of exon 1
TAAGTGCGTCTCCGATGAAATCCAACACAACGTCGTCGTTTTGGCCGACTACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgta---cccttttgcgatttctctactgcctccttcttcaattactcattcgtctgtttgcttccttgatttgcgtgttgacggatttgttttctcctggatt
 |||||||||||||| |||||||||  ||||||| ||||||| || || ||| | |||||| ||   || ||  |   |  ||  ||  || |||| ||||||      ||| |  |      | ||  |   ||| |  |||    | ||     | | |    ||  |||           |  || | ||| ||| ||  
AAAGTGCGTCTCCGAAGAAATCCAAAGCAACGTCATCGTTTTAGCTGATTACCTTGTTATCTCCGAGGAACATTCTATCTTCCCTACTGTCTCCGTTAAGgtaaagtaatttcgtaaaggacttgctttcatgttcgttgattg--gaatctgaactctacgaaattagtttctaaaaatggtgtcttatcttcaccttgaa-

upper sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv12s0034g01440.t01 (Vitis vinifera), 5'ss of exon 1
TAAGTGCGTCTCCGATGAAATCCAACACAACGTCGTCGTTTTGGCCGACTACGTCGTTATCCCCAGTGATCACGCCCA---CAACCTCACCATCGCCGTCAAGgtacccttttgcgatttctctactgcctccttcttcaattactcattcgtctgtttgcttccttgatttgcgtgttgacggatttgttttctcctggatt---
   |||||||||||| ||||||||  |||||||||||||||||||||| ||| |||| |||||    || ||  ||||   || || ||||||| || |||||||    |||| |  |  | | | |    ||   |||    |        |  || |    || || ||||  ||| ||   |  |            |||   
---GTGCGTCTCCGAAGAAATCCAGAACAACGTCGTCGTTTTGGCCGATTACCTCGTCATCCCAGACGACCATACCCATTCCAGCCCCACCATCTCCATCAAGgt-ttgtttttctttgcccccagtttaccccctttcgtccatcttcaaattcgtctttgaccctg-tttggttgtagagaaaactagggaaatg-aaattaat
















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|151394340|gb|EV264211.1|EV264211
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|193674695|gb|FK620363.1|FK620363
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATTCTACAAGGAGAACACAACAC
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCA-TC-ACAAGGAGAACACAACAC
EST: gi|151394089|gb|EV263960.1|EV263960
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|192306615|gb|FG998055.1|FG998055
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|209708754|gb|BW683778.1|BW683778
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|298176386|gb|HO023087.1|HO023087
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|298170194|gb|HO018818.1|HO018818
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCGTCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|298164598|gb|HO014243.1|HO014243
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTTAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|298173881|gb|HO017217.1|HO017217
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT
EST: gi|298176262|gb|HO015667.1|HO015667
EST:     ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAG                         GTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAGCACAACACAT
genomic: ACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtaccctttt ... tttactttagGTGACATCACCGTATGGAAACAATCTTCATCACAAGGAGAACACAACACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGTGCGTCTCCGATGAAATCCAACACAACGTCGTCGTTTTGGCCGACTACGTCGTTATCCCCAGTGATCACGCCCACAACCTCACCATCGCCGTCAAGgtacccttttgcgatttctctactgcctccttcttcaattactcattcgtctgtttgcttccttgatttgcgtgttgacggatttgttttctcctggatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc