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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatgcaatatatacttatatggacctgatttcctgctctttataaattttattacctttttttaatcataaagatggattttattgctattgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG

Basic information

species Glycine max
transcript GLYMA03G40840.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g42900.1 (Oryza sativa), 3'ss of exon 5
gtgatgcaatatatacttatatggacctgatttcctgctctttataaattttattacctttttttaatcataaagatggattttattgctattgt-ggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
  |      | | |     | ||  |   |     |  |  || ||  ||| |    ||  ||        |   |  ||| |   |||    ||    || | || ||  | |||||||||||||| || |||||||||||||| |||||| ||||||| || ||||| ||||| ||  |  |    ||||| || || |
--gtcagtttttgttgcactttgagctaaacacgatagtacttttatctttaaaatgctaattcacgaggcagctactgatatg--tgcatccgtcaaaagGTTACACACAACATGCAAATTCCTCTCTCCTATGCTGATGCTGTGATTGGAGCAGCTGGTGCTAGTATTAGCTATATTCGTAGGCACAGTGGTGCAACAG

upper sequence: GLYMA03G40840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G130095_T02 (Zea mays), 3'ss of exon 3
gtgatgcaatatatacttatatggacctgatttcctg--ctctttataaattt-tattacctttttttaatcataaagatggattttattgctat-tgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
|| |     || | | ||   ||   || || |  ||   | |||  |    | | | |   |   ||   | |||   |    ||  |   | | |  | ||| | || ||    |||||| ||||||| || |||||||||||||| || ||  ||||||| || ||||| ||||||||| |  |   |||||| || ||| 
gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA

upper sequence: GLYMA03G40840.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G04610.1 (Arabidopsis thaliana), 3'ss of exon 5
------------gtgatgcaatatatacttatatggacc---tgatttcctgctctttataaatttta--ttacctttttttaatcataaagatg---gattttattgctattgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
                ||||| || |  | |  | |||      || | ||||  |||||  || | |  | |     |   ||||  |  | ||   |  ||| ||  | |||  |||  | |||||||||||||| ||||| || ||||||||||||||||| ||||| ||  | ||  |||  ||||||||||  |||||   |||||| || |   
gtattccgccaatctctgcaacatgttatgaagttgactgttcaatctactgcaatttatgtatgtaaagtaaatcaatgaaaatctgagtggtgtggggatttgtttgttttgcagCAAGTTACGCAGCAAATGCAGATTCCACTGTCTTATGCTGATGCTGTAATTGGGACGTCGGGTTCAAACATAAGCTACACTAGACGTCTTAGTGGAGCAA---

upper sequence: GLYMA03G40840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0081g00440.t01 (Vitis vinifera), 3'ss of exon 6
gtgatgcaatatatacttatatggacctgatttcctgctctttataaattttattacctttttttaat-cataaagatggattttattgctattgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
   ||      |  ||    | |    || |  |   | |||  | | |  | || | | |    | |   | ||    ||  | ||  |  || | |||| | || || |||||||| |||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||| || || ||||||||||| ||||
cgaattttggttgaacaagca-gtttttgctcactctcacttcctgagtcctgttccttctaaaaagtgtttgaactctgaaataatctcattttttgcagGTAACACAACAAATGCAGATTCCTCTGTCTTATGCTGATGCCGTTATTGGAACAGCTGGTGCAAGTATAAGTTACATTAGGCGTGCTAGTGGGGCAACTG

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|19347622|gb|BM892480.1|BM892480
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|15286643|gb|BI470534.1|BI470534
EST:     TTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: TTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|192331608|gb|FK019969.1|FK019969
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|6846986|gb|AW349276.1|AW349276
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGNNNNNTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|12687962|gb|BG154237.1|BG154237
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|31311368|gb|CD396571.1|CD396571
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|4314126|gb|AI461245.1|AI461245
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|193703833|gb|FK634763.1|FK634763
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTA
EST: gi|192328162|gb|FK020423.1|FK020423
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|192325182|gb|FK019098.1|FK019098
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCA-CTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTCATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|16105469|gb|BI893209.1|BI893209
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATTGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|193543926|gb|FK503343.1|FK503343
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|16345362|gb|BI970957.1|BI970957
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|51343089|gb|CO983822.1|CO983822
EST:     CTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: CTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|254332499|gb|GR846437.1|GR846437
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAG                         ATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA
EST: gi|10848043|gb|BF070607.1|BF070607
EST:     GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAACCACACAG                         ATCACGCAGCAGATGCAAATTGCTCTATCTAATGCTGATGCTGTTATTGGA
genomic: GTGTTCATGCATCTTCAAATACTCAATCTGCACCTTCCATAGTCACACAGgtacttgttc ... attgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattttattacctttttttaatcataaagatggattttattgctattgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG
                ttttaat  putative branch site (score: 3)
             tttttttaatcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgcaatatatacttatatggacctgatttcctgctctttataaattttattacctttttttaatcataaagatggattttattgctattgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
-tgatgca
- - - - - - - - - - - - -cctgatt
- - - - - - - - - - - - - - - - - ctgctct