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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 3
gtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG
                                      ||  ||   |   ||| || |||     | ||||     || | ||||   |   |  |   ||  |  |    |    ||||        | ||||||||| |||| ||||||||||||||||||||||| || |||||||| ||  |||| ||||||||||| ||||||||||||||||||||||||||||| |||
--------------------------------------atgggaaaatg--ttaagaattgtatggtaccatattgcatttttcttgcatttcagtgcaattagggtatgtatgaccccaa---agtttgcctgttcttgcagGTTAAAGCAGTTGGAGAGGAAATGGGAATAGGATTTCTTGGGCTTGGCTTTCAGCCAAAATGGGCACTGAGTGACATACCAATAATGCCAAAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 3
gtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG
                                     || | |  | | |      | || |  | |  | || |||  | || |   ||     |||    |||   | |  ||| |  |        || |||||||||||||||||||||||||||| |||||||| || |||||||| ||  |||| ||||||||||| |||||||||||||| |||||||||||||| |||
-------------------------------------tactagggtcttatgggaaaatttcaaaattgcgtggcattaaaatgtattgtttc--agtgcaattgggggta--tgacctca--aagtttgtttgttcttgtagGTCAAAGCAGTTGGAGAAGAAATGGGAATAGGATTTCTTGGGCTTGGCTTTCAGCCAAAATGGGCACTGAGTGATATACCAATAATGCCAAAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 4
gtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG
                                      ||||  |  |   || |  | |  | ||     ||  || |  |        |  |     |||    | | | ||  | | ||   |       ||  || ||||| ||||| ||||  ||||||||||| ||||||||| | || |||||||| ||||||||||||| | | |  |||||||| |||||||| |||
------------------------------------aaatttagtactagtttgttgtgtttg-atgtttctgttatctg-acaagtgaccttatgacctttaaatcggtaattatttccatataa-----tcgtgtttatagGTTAAAGCTGTTGCTGAGGAAATGGGAATTGGATTTTTGGGGATTGGTTTCCAGCCAAAGTGGGGAATCAAAGACATACCTATAATGCCAAAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 4
gtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG
                                      ||||  |  |   || |  | |     |||    | |   ||| |    |||       |||  ||   | | ||  |   | |  || |      |  || ||||| ||||| ||||  ||||||||||| ||||||||| | || |||||||| ||||||||||||| | | |  |||||||| |||||||| |||
------------------------------------aaatttagtactagtttgttgtgt-----ttgatgagtctgttatctgacaagtgaccttatttccttcaaaacggt--aattattttgatatactcatgtttatagGTTAAAGCTGTTGCCGAGGAAATGGGAATTGGATTTTTGGGGATTGGTTTCCAGCCAAAGTGGGGAATCAAAGACATACCTATAATGCCAAAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 4
gtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG
                                  | |||||||  |||  ||| || |||  | | |  | |   |||   || | | ||  |  |     || |  |     ||       |  |    | |||| |   |||| |||||||||| |||||||||||||||||||||  | || |||||||| ||||| || |||||  | |  || ||||| ||||||||||||
---------------------------------acattatttgtgtttagctt-tggtttttgaaatctcttaagata-ggatataccgtatgctacgaacttggttattgtctg-------ctaatgtttttgtt-taacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTCCAGCCCAAATGGGCTATTAAAGATATACCTATAATGCCCAAG

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|7219950|gb|AU063307.2|AU063307
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|33796283|gb|CF324008.1|CF324008
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|88347509|gb|CI637449.1|CI637449
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGG
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGG
EST: gi|88573359|gb|CI664930.1|CI664930
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTG
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTG
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
EST: gi|88336064|gb|CI647258.1|CI647258
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAA
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAA
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAG                         GTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT
genomic: TTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgca ... gttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtagGTCAAAGCAGTTGGAGAGGAAATGGGGATTGGATTTCTCGGAATTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG
                      agttgat  putative branch site (score: 5)
                                          tctgttctt  putative PPT
     aaagttttttt  TA-rich tract