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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT

Basic information

species Glycine max
transcript GLYMA08G21380.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 6
gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
     |||||  | |    |||| | | ||  | ||    |          |   || | | || |  || || |    ||    ||| |  ||  | || | | |  || |       || ||||||| ||||||||||| ||||| ||||| || || ||||||||||| || ||||| ||  |  | |
---gccatttcttctagcggtgttaaaaaacaatcacatgt----------gctgttgcatatgctaatctaatag---tgcttcaaaggtatg--ttgatcaatttgttgtc------tgtagATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT

upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G16480.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
                                          |    |  |     ||| ||  ||| ||    ||      |  |  | ||||  |  ||     |||||||        ||||||||||||||||||||||| ||||| || || || || ||||||||||| ||||||||  |||| |
------------------------------------------gtgcctgactcaaatacattacttgatctttcaaacgcaaa-gacttaattgtgtaaaatc--caattcttat------cagATGCTTATGGGAGGAGGTGGCTCATTTTCTGCGGGAGGCCCTGGAAAAGGAATGCACTCTTGGCTCT

upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatg--cagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
                 | || | || ||| |   |   |||||||  ||   | || |  |||||  || |  || | | |   |   |    || | ||  ||   |  |  |||       |||||||||||||||||||||| |||||||| || || || ||||||||||| ||||||||  |||| |
-----------------gtgtctaattgaatt-ttactttttggttgctttaacttt-cacttgtt--tcgatcaaattttttttactggcgaaaaagtaataaaatgtaatctaattgctattagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT

upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------gtacacattttgtgtctgagtgtg-atagaaatac-catgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
                                                       | |  | | | |||   | |  ||| | |||   ||   |   | | ||| |  |  || || |   |||   |   ||||      |  ||   || |   |  |||     | ||  |||||||||||||||||||||||| |||||||| || ||||| ||||||||||| ||||||||| | ||||
gtgctgcatttgatcttttcttcttaaagagattctgctatctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatattcatattccctcttttcattcatccac-catgttt----tccttttttgcattaagaaatgtgatagtcccgcagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGGGGCCCTGGAAAAGGAATGCACTCACGACTAT

upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------gtacacattttgtgtctgagtgtgatagaaataccatgctttggttttttcgtccttacttttgttgctcaaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
                                                                     | |  | | | |||   | | ||| | |||  ||   |   | | |   |  |  || || |   |||   |   ||||      |  ||   || |   |  |||     | || ||||||| ||||||||||||||||| ||||||||  | ||||| ||||||||||| ||||||||| | ||||
gtgctgcatttgatcttttcttcttaaagagattctgctatttggaaatctctctctctctctctctctctctctctctctctatatat-atatatatat-atatatatatatatatatattccctcttttcattcatccac-catgttt----tccttttttgcattaagaaatgtgatagtcctgcagATACTTATGGGAGGAGGTGGCTCATTCTCTACGGGGGGCCCTGGAAAAGGAATGCACTCACGACTAT

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|17023865|gb|BM094899.1|BM094899
EST:     CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAG                         ATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
genomic: CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAGgtacacattt ... aatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
EST: gi|254320746|gb|GR827195.1|GR827195
EST:     CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAG                         ATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGG-CCTGG
genomic: CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAGgtacacattt ... aatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGG
EST: gi|13562687|gb|BG550907.1|BG550907
EST:     CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAG                         ATGCTTATGGGAGGAGGTGGGTCATTCTCAGCATTGGTGGCCTGGAAAAGG
genomic: CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAGgtacacattt ... aatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGG-GGCCTGGAAAAGG
EST: gi|38192388|gb|CF921594.1|CF921594
EST:     CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAG                         ATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
genomic: CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAGgtacacattt ... aatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
EST: gi|38193674|gb|CF922880.1|CF922880
EST:     CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAG                         ATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
genomic: CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAGgtacacattt ... aatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
EST: gi|8282640|gb|BE020201.1|BE020201
EST:     CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAG                         ATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG
genomic: CTGGTGGCTGGCAAAAGGAGAAAGATGCTATTGTTTTGACTGTTTTACAGgtacacattt ... aatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaaaagtatgtacaaaatgattgaatggaactaataattcttgaatcatgcagATGCTTATGGGAGGAGGTGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT
                              aactaat  putative branch site (score: 2)
                                 taataattcttgaat  TA-rich tract