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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTTGGGGATGCTTCCAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgtacttgtttttctcccaattatttttactagtggttattcaatcatcattggattttttttgcctttccatttgattcatgtttatgtttt...

Basic information

species Glycine max
transcript GLYMA08G26000.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26000.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g66170.1 (Oryza sativa), 5'ss of exon 5
TTGGTTGGGGATGCTTCCAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgta-----cttgtttttctcccaattatttttactagtg--gttattcaatcatcattggattttttttgcctttccatttgattcatgtttatgtttt
||||||||| |||||||||||| ||||||| ||||||||||||||||| |||||| |||| |||||||| ||||  ||      |||  ||  |     | |||   |  |     ||  ||| ||   ||||  ||   || ||   ||| ||   |  ||  | |||     
TTGGTTGGGAATGCTTCCAGGATCATGGGCCTATGTCAGTGCTGGTGCATTTGGACGAGCTATAATTgtaagttcttaaacacattgaattattttagttcattgccagcacaaacgtacttccattgccatttcatccattctg---ttcaatgaaaaccacatctatt----

upper sequence: GLYMA08G26000.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G011479_T01 (Zea mays), 5'ss of exon 5
TTGGTTGGGGATGCTTCCAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgtac-ttgtttttctcccaa--ttatttttactagtggttattcaatcatcattg-gattttttttgcctttccatttgattcatgtttatgtttt
||||||||| |||||||||||  |||||||||| ||||| |||||||| || ||  |||| |||||||||||||  ||   ||  | | |   ||    || ||   ||     | | |   ||  || |  |       |  || |  | | |   |||  || ||    
TTGGTTGGGAATGCTTCCAGGTTCATGGGCTTACGTCAGCGCTGGTGCATTCGGGCGAGCTATAATTgtgagttcttaaactgcctgtattttaagtccatcttcgttaaaaaatgtacttccaaaatggcaaaagaggattgctatgtaatagccacattattgtg----

upper sequence: GLYMA08G26000.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G068271_T01 (Zea mays), 5'ss of exon 6
TTGGTTGGGGATGCTTCCAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgtac-ttgtttttctcccaattatttttactagtggttattcaat-catcattggattttttttgcctttccatttgattcatgtttatgtttt
||||||||| |||||||||||  |||||||||| |||||||| ||||| || ||  ||||  |||| |||||||  ||   || |  | |   || |   | | |  | |   |   | | ||       | |      |    |    | |  |  |    |  ||| 
TTGGTTGGGAATGCTTCCAGGTTCATGGGCTTACGTCAGTGCCGGTGCATTCGGGCGAGCTTTAATCgtgagttcttaaactgctggtattttaagtccatcttcaggggaaaaaaaattgcactgccaaaatggcaacgaggatttgct-gtgtagtaaccacattt-

upper sequence: GLYMA08G26000.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0001g03830.t01 (Vitis vinifera), 5'ss of exon 5
TTGGTTGGGGATGCTTCCAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgtacttgtttttctcccaattatttttactagtggttattcaatcatcattggattttttttgcctttccatttgattca--tgtttatgtttt---
|||| |||| |||||||| ||||||||||||||||| ||||||||||| |||||  ||||||| ||||||||||| |  |||  ||   |     |  |  | |   |  |      ||||   ||   |||||  ||| |    |    ||  |  | || |||   |   
TTGGCTGGGAATGCTTCCTGGAACATGGGCTTATGTGAGTGCTGGTGCATTTGGGCGAGCAATCATTgtgagtttatcattggcttatcc-----tgctactgcatatcatacacttatcacttttaattttttactgcttactaaacaaataaaaatattaatgacctttt

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|151405427|gb|EV275241.1|EV275241
EST:     CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATT                         CGAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACGGTCAGTTGCTG
genomic: CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgt ... tacatttcagCAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
EST: gi|13478933|gb|BG508276.1|BG508276
EST:     CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATT                         CAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
genomic: CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgt ... tacatttcagCAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
EST: gi|208337682|gb|GE136478.1|GE136478
EST:     CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATT                         CAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
genomic: CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgt ... tacatttcagCAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
EST: gi|6914740|gb|AW396270.1|AW396270
EST:     ATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATT                         CAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
genomic: ATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgt ... tacatttcagCAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
EST: gi|209699649|gb|BW655728.1|BW655728
EST:     CAGGAACATGGGCTTATGTCAGTGCTGGTGC-TTTGGAAGAGCAATAATT                         CAAGATGAATCTGAACTTAGTAATATA-TTGGAGGAAACAGTCAGTTGCTA
genomic: CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgt ... tacatttcagCAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
EST: gi|51337968|gb|CO981834.1|CO981834
EST:     CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATT                         CAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA
genomic: CAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgt ... tacatttcagCAAGATGAATCTGAACTTAGTAATATATTTGGAGGAAACAGTCAGTTGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTTGGGGATGCTTCCAGGAACATGGGCTTATGTCAGTGCTGGTGCTTTTGGAAGAGCAATAATTgtgagtttgtacttgtttttctcccaattatttttactagtggttattcaatcatcattggattttttttgcctttccatttgattcatgtttatgtttt

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc