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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT

Basic information

species Glycine max
transcript GLYMA17G13850.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
---caatt---aataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
    | ||    |   ||  | ||| || | | || | | |||| ||  ||| |||  || |  ||||       ||  |||   |   || |   ||   ||||||| ||||| || ||  |  | ||||| || ||||| ||||| ||||| |||||||| |||||| | || |||||||| |||||||||||||| ||||| |
ctatattttgggacggatggagtattatat-gttggctacctaattt--tctctatttaagtcctatcttaaaaattgcctctggt---aaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
----caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
    ||||      || |  |     |  | |  | ||  |||   |  |||| |  |     | | |     |||| | |  | |    ||   | |   ||||| || ||||| ||  || | ||||| || ||||| ||||| || ||||||||||| |||||  | || ||||| ||||||||||| ||||| ||||| |
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaac---ttatgttgtttatattctattctatac-cagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatc--tcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
 | ||       || | |||||| |  |  || |  || ||| |  ||| |   ||  |||      |   | |||  ||  ||||   |   ||||  ||||||| || ||||| || || |||||||| || ||||||||||| || || ||||||||||| ||| | || |  ||||||| ||| |||||||||||||| |
-atttggctttcctca-ataattcttctctcc-taaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtcttt-atgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatctcgactctgaattaccttt-tgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
 | ||       || | | |||||  ||  || | ||| ||     ||| |   ||  |||      |   | |||      ||    ||| | | |   ||||| || || || || || |||||||| ||  |||||||||| || || ||||||||||||||| | || || ||||||||||||||| |||||||||| |
aatttggctttcctcaaaaaattt--atctcc-tataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
caattaataaatct-aatata--attttgatgaccatctaac-ttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
|| || || |  || || | |  | ||  |  || |||     ||| |||||    || | |  || |       ||||        ||||      ||||||||| ||||| || || ||  ||||||| ||||||||||| || || ||||||||||| |||||  ||||||||||||||||||| ||||||||||| ||||
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgc--aattgtgttctaaggaacaatcttagtgt--aattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
                                             | | |     | ||||    | | ||   | |  ||| |   |  | |   |||||| || |  ||  | || ||||||||||| || ||||||||||| || |||||||| |||||  ||||||| || |||||||| || |||||||| ||||
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttg--tctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
                                             | | |     | ||||    | | ||   | |  ||| |   | || |   |||||| || |  ||  | || ||||||||||| || ||||||||||| || |||||||| |||||  ||||||| || |||||||| || |||||||| ||||
--------------------------------------------gtctgtgtgtttgttatttgctttttttctttg--tctaacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|21995058|gb|BQ786586.1|BQ786586
EST:     GCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAG                         CCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: GCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAGgtttcacttc ... ttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|16277629|gb|BI942480.1|BI942480
EST:     TGCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAG                         CCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: TGCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAGgtttcacttc ... ttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|298164997|gb|HO011046.1|HO011046
EST:     TGCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAG                         CCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAGCAATG
genomic: TGCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAGgtttcacttc ... ttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|254327049|gb|GR836658.1|GR836658
EST:     TGCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAG                         CCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: TGCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAGGGACAATTAACCAAGgtttcacttc ... ttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
EST: gi|192294988|gb|FG986707.1|FG986707
EST:     GCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAAAGGGACAATTAACCAAG                         CCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAA
genomic: GCTTCCTTTACAGAGGCCTGAGCTTTTTTGCAA-GGGACAATTAACCAAGgtttcacttc ... ttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAA
EST: gi|298163750|gb|HO012483.1|HO012483
EST:     GCTTCCTTTACAGAGGCCTGAGCNNNNNNNGCAAGGGACAATTAACCAAG                         CCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG
genomic: GCTTCCTTTACAGAGGCCTGAGC-TTTTTTGCAAGGGACAATTAACCAAGgtttcacttc ... ttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
                                        ttacctttt  CT-rich tract
      aaaatattatccatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - ccatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgaa