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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT

Basic information

species Zea mays
transcript GRMZM2G423456_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g69920.2 (Oryza sativa), 3'ss of exon 4
gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                                             | ||  ||||  |    |    ||| | ||| |     ||  | |    | |  |  | | |  | || |||   | ||   |||      ||||| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||                                                
-------------------------------------------gtttttagtcttacatctcacttccttctgcttgcacacatccttct----gagttaggata-gacatctcact---tcatacgttc------ttttccgcttgcagTTCTTGGCTACTGTTTCACATGAGATCAGAACTCCAATGAATGGTGTTCTAG------------------------------------------------

upper sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G11060.2 (Glycine max), 3'ss of exon 6
gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttact-accttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                                                           |       ||| || |||    | | | | ||||            |     | |||| | | | |    |   |  |  || |    ||||||  | ||||||||||| |||||||||||||| ||||||||||||||| | |                                                
-----------------------------------------------------------gtatggaactt-ttttttaaaatttatttgttgaacttattttggcttaactcatactgatcatgtgggctt--tatcaattgtaaccgcagTTTCTTGCTACTGTTTCCCATGAGATCAGAACACCAATGAATGGTGTTTTGG------------------------------------------------

upper sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G28070.1 (Glycine max), 3'ss of exon 5
gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttact-accttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                                                          |     |   || ||  ||  | | | | ||||||            |     |  ||| | | | |    |   |  |  || |     |||||  | ||||||||||| ||||| |||||||| ||||||||||||||| |||                                                
----------------------------------------------------------gtatgtaactttatttatttatttatttattttgaacttgttttggcttaactcacactgatcatgtgggctt--tatcaattgtaaccacagTTTCTTGCTACTGTTTCCCATGAAATCAGAACACCAATGAATGGTGTTTTAG------------------------------------------------

upper sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G27320.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                                         | | |   ||      ||  || |   ||   |       |     || |  |      | ||  | |               ||||  ||   ||||| |   |||||||| | || |||||||| ||||| ||||||||||||||||||||||||||||                                                
----------------------------------------gtaaatacatcatcctcagttgataaatttccacagcatattaaactttctatgacagagagaagagttg--------------taatctaa---cttttttttatgcagTTCCTTGCCACTGTTTCACATGAAATCAGAACTCCAATGAATGGTGTTCTAG------------------------------------------------

upper sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0010g03780.t01 (Vitis vinifera), 3'ss of exon 5
gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaag-gcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                                     |||||||   |||   |  |    |  || ||||||| |  | |  |                  | | || |    | |||   |   | ||||| |   | |        ||||| | || ||||||||||||||||||||||| ||||||||||||||||| |                                                
------------------------------------gtatttgatgcttttagtcaacttactgaaagcttgttttggcttaacctatc-------------acagtgatttagttctaa--tgaaagttcaacgttctat--------agTTCCTTGCCACTGTTTCTCATGAGATCAGAACCCCAATGAATGGTGTTCTCG------------------------------------------------

upper sequence: GRMZM2G423456_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgaatagcttcgctgcaaataatagctatgcatgcttatttgactgtttctcttgaaggcgaaaggcttgttctttcctctctctcttttgaggggccaaaaaatggtaccttactaccttattaattcaatgcctt-ttctgcttg--cagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                                                     || |      |    ||  | ||   |   | |||   |       |||| |   || |  || | | |   |   | |    || ||   ||||  ||||||||||| ||||| ||||| |||||  | ||||||||||||||||||||||                                                
-----------------------------------------------------tttattatttattattttattttattttattttctcacgtaaaaataaaacaaaataacacacaagcatgaaataacgacttgttgttgaacttgtgcagTTCTTGGCAACTGTGTCTCACGAGATTCGGACTCCAATGAATGGTGTTCTAG------------------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccaaaaaatggtaccttactaccttattaattcaatgccttttctgcttgcagTTCTTGGCTACTGTTTCTCATGAGATCAGAACTCCAATGAATGGTGTTCTAGGTGAGGTTCTAGTCCATCTAAACTGTACAATAATCTTAATTGTTAATT
                          tattaat  putative branch site (score: 2)
                                     tgccttttctgctt  putative PPT
                         ttattaattcaat  TA-rich tract