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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttattcctggagttttttctttgcctaaatagttttcatactgtatcttattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC

Basic information

species Glycine max
transcript GLYMA10G34240.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G006965_T01 (Zea mays), 3'ss of exon 4
--tttttattcctggagttttttctttg-cctaaatagttttcatactgtatcttattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC
| | || | | |||| | || | || ||| ||||| | || | | || | | | ||| || | ||||| |||||| || |||||||||||| | || ||||| ||||||||||||||||||| || ||||| ||||||||||| || |||||||||||||| |
atagtaggctaatgcactcaactcttcgatttatagtaagtttggggagtagcttat--atgttatgtgtggcaaag-gctcatatttttcttttctgtccagGAATGGGAGGCTATCAATGATTTAAGAGCTGATATGGCTAGACTTCAGCAAGGCATGAGCCATATGCAAAGGATGTTGGAAGCTTGCATGGATATGCAGC

upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G081965_T01 (Zea mays), 3'ss of exon 4
---------------------------tttttattcctggagttttttctttgcct----aaatagttttca--tactgtatcttattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC
|| | | ||||| |||| | | ||| | |||| | || || | | |||| | || || ||||| ||| | | ||| ||||| ||||| || |||||||||||| | ||||||| |||||||||||||| |||| ||||||||||||| |||| || |||||||| ||||| |
gtacatgcagatcctatgctatcttcacattcaataatggagcttttgtatagaaggagaaaaaactttttaactagtgcgttgagtcaaaaaaaagtaatatatt-tggttctgt--gtttcttg----cagGAATGGGATGCTATTAATGATTTAAGAGCTGACATGGGTAGACTTCAGCAAGGGATGAGCAGCATGCAGAGGATGCTGGAAGCGTGCATGGACATGCAGC

upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G04460.2 (Arabidopsis thaliana), 3'ss of exon 5
----tttttattcctggagttttttctttg----cctaaatagttt-tcatactgtat--cttattaaaattctttttga----tgttctg---gttttgtt-tgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC
| || | ||||| | | | | || || || | || || || | ||| | || | || | ||| || | ||| | | || | | | |||| |||||| ||||||| || ||||| |||| |||||||||| |||||||| |||| || |||||||||||| | || |||||||||||||||||
gtaatccttccattgagggttttagcctcgagtccttagctaattaattatgctcaatgacatatcataagcttggttaaaaggtgtaatgtagatattgctcttcttggttgcattagGAATGGGAGGTAATGAACGACCTAAGAGGAGACGTGGCAAGACTGCAGCAAGGAATGAGCCAGATGCAGAGGATGCTTGAAGCCTGCATGGATATGCAGT

upper sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 4
--tttttattcctggagttttttctttgcctaaatagttttcatactgtatct-tattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC
| || | || | || || || | || | || | | || ||| || || | || |||||| ||| ||||| ||||| || || |||||| | ||| |||| ||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||||||||
cacatacatgtcaatcccaaacctattaaagatattgtgtttgtgctagacctatttcaatatttcccagtttgaacttagtgtgcatgctgacatggagCAGGAATGGGAAATGATTAATGATCTGAGAGCAGATATGGCAAAGCTTCAGCAAGGCATGAATCACATGCAAAGGATGTTGGAGGCTTGCATGGATATGC---

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|298171118|gb|HO016150.1|HO016150
EST:     ATTTGCATCAAACTGGATGGTCTCGCCATAGCATGCATCGTTCTGAAATT                         GAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAA
genomic: ATTTGCATCAAACTGGATGGTCTCGCCATAGCATGCATCGTTCTGAAATTgtatgcatct ... ttgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAA
EST: gi|192314587|gb|FK008123.1|FK008123
EST:     ATTTGCATCAAACTGGATGGCCTCGCCATAGCATGCATCGTTCTGAAATT                         GAGTGGGAGAT
genomic: ATTTGCATCAAACTGGATGGTCTCGCCATAGCATGCATCGTTCTGAAATTgtatgcatct ... ttgggaacagGAGTGGGAGAT
EST: gi|192314588|gb|FK008124.1|FK008124
EST:     ATTTGCATCAAACTGGATGGCCTCGCCATAGCATGCATCGTTCTGAAATT                         GAGTGGGAGATAATGAATGATTTA-GATCAGACATGGCA-GACTTCAGCAA
genomic: ATTTGCATCAAACTGGATGGTCTCGCCATAGCATGCATCGTTCTGAAATTgtatgcatct ... ttgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcttattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC
                                       tgctgat  putative branch site (score: 3)
 ttattaaaattctttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttattcctggagttttttctttgcctaaatagttttcatactgtatcttattaaaattctttttgatgttctggttttgtttgctgattgggaacagGAGTGGGAGATAATGAATGATTTAAGATCAGACATGGCAAGACTTCAGCAAGGCATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - -tcctgga
- - - - - - - - - - -ctttgcc
- - - - - - - - - - - - - - - - - - - -catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctga