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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttagttgtgcaaac...

Basic information

species Glycine max
transcript GLYMA20G31730.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g34560.1 (Oryza sativa), 5'ss of exon 3
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgctta-gttgtgcaaac
||||  || ||||| || ||||  || || ||||| ||||| || || |||||||| || ||||| |||||||||||||| ||||||||||||||||||||||      || |  |  ||| || || || |   |   |||  |  |   | | |   || ||  ||  ||         | |  ||| ||  |    ||
ATATGCTACCCTGCTATTGAGAATCACGAATGGCGTATTGTGACAGGCTGTGATCCGAAGAATACTAGATGGAGTTACCACAATGGAGGATCTTGGCCAGgttagaaggttttcttattat-ttaaatctctcttaaatattacagtttttagtcgcaaaaatgttatcatgcttcccttttatcattatgtgatttggac

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G170842_T01 (Zea mays), 5'ss of exon 3
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatt----tggttaattgggattttgaccggtaggtgtgcttagttgtgcaaac
|||| ||||||||| || |||| |||||| ||||||||||| ||||| |||||||| |||||||| ||||||||||| || ||||||||||| ||||||||||  |     || | | |   ||      ||    | | |   |    | | |    |    ||| || ||  | |        | | ||   |  ||     
ATATGTTATCCTGCTATTGAGAACCATGAATGGCGAATTGTGACTGGCTGTGATCCAAAAAATACTAGATGGAGTTATCACAATGGAGGATCGTGGCCAGgttagtgaaaacttcactttggttgttctgttctctttcttcggacactgaactacaataaacaatgggaatcataatttaagtatatactggatgttgt----

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G118737_T01 (Zea mays), 5'ss of exon 3
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggt---taattgggattttgaccggtaggtgtgcttagttgtgcaaac
|||| ||||||||| || |||| |||||| ||||||||||| || || |||||||| ||||| || ||||||||||| |||||||||||||| ||||||||||  |    |   |    ||  |     ||     |      |   ||   |    |    ||| |||||  | |        | | ||   |  | ||   
ATATGTTATCCTGCTATTGAGAACCATGAATGGCGAATTGTGACGGGCTGTGATCCAAAAAACACTAGATGGAGTTATCATAATGGAGGATCGTGGCCAGgttagtgagcttcacatggattgttctttttctctttctgcggacactgaactacaataaacaatggggatgataatttaagtatatactggatgttcca---

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G115451_T02 (Zea mays), 5'ss of exon 4
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgt-tcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttagttgtgcaaac--
||||  ||||||||  | ||||  ||||||||| ||||| ||||||| ||||| |||||||| ||| | ||||||||||| ||||||||||||||||||||| || ||  |  |    || |    ||| ||| |  |    ||  | | || ||    |       | | | ||  ||   || |  ||  |||    |   
ATATGCTATCCTGCTCTCGAGAATCATGAGTGGAGAATTATTACTGGATGTGACCCCAAAAACACCCGGTGGAGTTACCACAATGGAGGATCTTGGCCAGgtatcgtctctcgttgcaatgtgactaaattttgacttttggtttgt-taggtttcaactctagcctactctaacttgtt--tgggtctaaatgtctttattg

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G007277_T01 (Zea mays), 5'ss of exon 4
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttagttgtgcaaac----
||||  ||||||||  | ||||  ||||||||| ||||  | ||||| ||||| ||||| || ||| | ||||||||||| ||||||||||| |||||||||     ||  ||   || |||||     |||    |      || || |  | |  ||  |    ||  ||    | ||  ||| |||| ||      |    
ATATGCTATCCTGCTCTCGAGAATCATGAGTGGAGAATAATCACTGGATGTGACCCCAAGAACACCCGGTGGAGTTACCACAATGGAGGATCGTGGCCAGgtatcatctccctttgca-atattttttgttttttttctggaaaaagtagc-tctaatt--tctatatcatgtgttgcagtagtggttagatgaatgcccgaga

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G22650.1 (Arabidopsis thaliana), 5'ss of exon 4
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccgg-taggtgtgct-tagttgtgcaaac-------
|| | | |||| ||||| ||||||||||||||| | |||||||| ||||| || || || |||||  | |||||||||||||| || || ||||||||||||   |   ||||| || |||| |    ||| ||| |  ||||        |     ||  |   |||  ||||    || || |  | ||  | |  |||        
ATTTGTCATCCGGCAATCGAGAGCCATGAGTGGAGGATTGTTACCGGTTGCGACCCTAAGAATACTCGTTGGAGTTACCATAACGGTGGTTCTTGGCCAGgtgaat---ttctgttc-tatacttt--cttgaaactatattttgaacaaaaccaatttttt---gatagtgacaaaataagtattttatatctttttaaataaccttt

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G09510.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttagttgtgcaaac
|||| ||| |||   || || ||||| |||||||| |||||||| ||||||||||| ||||| || || ||||||||||| || || ||||||||||||||||     | | ||    ||||   |||||   |||  |||    ||      ||||||  ||   | | |    | || |||                 
ATATGTTACCCTTGCATCGAAAGCCACGAGTGGCGGATTGTTACCGGTTGTGATCCTAAAAACACGAGGTGGAGTTACCACAACGGTGGATCTTGGCCAGgttagcattctttgt---tata---aaact---aaagacatcatgtgaaacgcttggttccttatcactatc-ttgatatgtgcag--------------

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G35580.2 (Arabidopsis thaliana), 5'ss of exon 5
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttag----ttgtgcaaac--
|| | ||||||     | ||| ||||||||||||| || |||||||| ||||| ||||| || ||  | ||||| ||||| ||||| |||||||||||||||  ||  | | | |    | | |   | |  |  |  |||||  | |     | | |||| || ||||||  |  |     |   ||||    || | |      
ATTTGTTATCCATGCCTCGAGGGCCATGAGTGGCGCATCGTTACTGGCTGTGACCCCAAGAACACACGGTGGAGCTACCACAATGGTGGATCTTGGCCAGgtcttttttctttccctggagact--gattgcatgagacatttcttat----ctcgcttaactgagattttcgctagacctagccattagggtttttttcggtttg

upper sequence: GLYMA20G31730.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv18s0072g01040.t01 (Vitis vinifera), 5'ss of exon 4
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgac-cggtaggtgtgcttagttgtgcaaac---
|||  |||||||||| | || | |||||| ||||||||  | |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||  |||||  |||| |    ||| |    |       ||||  |     ||    || |     || ||||  |  | |      || | | |         
ATAAGTTATCCTGCATTCGAAAACCATGAATGGCGAATCATAACTGGTTGTGATCCTAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgtttgtccttcttgcttaccgtttctagtgct----cctattttctcccaaatcatatttaacacaatgttgatgcaatggagacagttggctattgtgttgtg

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|254337771|gb|GR845341.1|GR845341
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|193607777|gb|FK557516.1|FK557516
EST:     GGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: GGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|14011212|gb|BG726134.1|BG726134
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|8284373|gb|BE021932.1|BE021932
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|58018148|gb|CX704890.1|CX704890
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|254327979|gb|GR834944.1|GR834944
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|10709954|gb|BF009678.1|BF009678
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|19936331|gb|BQ080819.1|BQ080819
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|193541022|gb|FK495680.1|FK495680
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|15203943|gb|BI426720.1|BI426720
EST:     CCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: CCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|37994477|gb|CF806223.1|CF806223
EST:     TTACCATATTGGAGGATCTTGTCCAC                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
EST: gi|37996959|gb|CF808548.1|CF808548
EST:     TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAG                         TGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA
genomic: TGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctt ... ttgagtgcagTGCTCCTGTGGCTAGTAACAGCTGCTTGTATCAAAACGGGGAGACCACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCTTATCCTGCAATAGAGAGCCATGAGTGGCGAATTGTTACTGGTTGTGATCCCAAAAATACCAGATGGAGTTACCATAATGGAGGATCTTGGCCAGgttcttcctttctgctcatatattcaaactttaaaatgcatttaatgtgggatttggttaattgggattttgaccggtaggtgtgcttagttgtgcaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT