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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcatttttatcaatattgatactatgaatttgtgctattctagatttccagttctcagcattctttctttatccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG

Basic information

species Glycine max
transcript GLYMA12G12960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G12960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G34050.1 (Arabidopsis thaliana), 3'ss of exon 2
gtattcatttttatcaatattgatactatgaatttgtgctattctagatttccagttctcagcattctttctttatcc--ttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG
||| | |  |   | |   ||| |  | |    || |  |  | |    ||    ||||     |  ||  | |  |   |||||||||||| ||||||||||| || ||||| |||| ||| ||||  |||||||||| |||||
gtaataacatcattaagccttgttcttgtttgattataatcctttgatcttttttttctttttctaattgatgttgcaaattgcagCCGATACTTTGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAG

upper sequence: GLYMA12G12960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g00660.t01 (Vitis vinifera), 3'ss of exon 2
gtattcatttttatcaatattgatactatgaatttgtgctattctagatttccagttctcagcattctttctttatccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG
||| ||  |||      ||||  |  | || || || |   ||||   |      |||| |      |   | |||||||| |||||  |||||||||||||||| ||||| |||||||| ||  | |||||||| | |||||
gtaatccatttacctggtatttttgttgtgtatgtg-gtctttcttattcctttattctta----cttccatctatccttgtagCCGGCATTTTGTCATTCCTTTGTGGAGAGGAAGTGGTTATGCAACAATGTTCGCTCAAG
















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|192331188|gb|FK020955.1|FK020955
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|192300166|gb|FG989288.1|FG989288
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|17400249|gb|BM177040.1|BM177040
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAAAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|192331203|gb|FK020956.1|FK020956
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|8827322|gb|BE211052.1|BE211052
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|298179061|gb|HO024796.1|HO024796
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|254320768|gb|GR827217.1|GR827217
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|254320769|gb|GR827218.1|GR827218
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
EST: gi|19453517|gb|BM954927.1|BM954927
EST:     ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATG                         CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT
genomic: ACTATGAAAGCAAAACTTTATCACTTGCTGGAGCATAGAGCTTCAGAATGgtattcattt ... atccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttgtgctattctagatttccagttctcagcattctttctttatccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG
                                 cattctttctttatcc  CT-rich tract
                                      tttctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcatttttatcaatattgatactatgaatttgtgctattctagatttccagttctcagcattctttctttatccttgcagCCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA