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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaagaggtgctatgttgtatgtagtgggctagtggcttcataaatttgtttgagaaagaaatgcatagactaattaataaatgtaacatgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGCCAGCATCACAGGCTGTTGAAGAACAAGCTGCTGCCACAGCATAGTGTGT

Basic information

species Glycine max
transcript GLYMA17G34690.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 15
---------------------------ttgaagaggtgctatgttgtatgtagtgggctagtggcttcataa-----atttgtttgagaaagaaatgcatagactaattaataaatgtaacatgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGCCAGCATCACAGGCTGTTGAAGAACAA---GCTGCTGCCACAGCATAGTGTGT
                            |    |  |||||  ||      ||   |    |  ||    ||       | || |  |      ||    |   || ||   || | |    | |  | |||||||||| || |||||||| |||||||||||||| | ||| ||||||||  || |||| ||||| |  ||||||||    || || || |||||||||     
gtatgcacacttctgcaaatggttccagttctaatatgcta-attccccacagcttgtccatatctctgaaatgagtgctggtatatgttgatgatagtgactttacttttaaattttgttttatcaaccagGACGTGTGGACAATGTGTATGGTGACCGCAACCTCACTTGTACCCTTCTTTCACCATCCCAGGCAGCGGAAGAACAGAAGGCGGCAGCTACAGCATAGGC---

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 14
----------------------------------ttgaagaggtgctatgttgtatgtagtgggctagtggcttcataaatttgt-ttgagaaagaaatgcatagactaat--taataaat----gtaacatgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGCCAGCATCACAGGCTGTTGAAGAACAAGCTGCTGCCACAGCATAGTGTGT---
                                  | ||  |    ||||| | | || |     | |  |  ||| |   | | | || |||| |   ||| |    ||||   ||  | |     |  |   |   |||||||||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||||    |||||||||||||||| || || || |||  |     
gtatctatctgactgcctttttgctccaaccatgtcgattaaac-ctatgat-tctgcaaatttccacagttttcttcgttctttctttagaatgccctgcttgatttaatagcaacgattttttattgctgatccttcagGACGTGTTGACAATGTGTACGGTGACCGCAACCTCATCTGCACTCTTCTTCCAGCATCACAG---ATTGAAGAACAAGCTGCAGCTACTGCCTAGGCTTCAGC
















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|209722170|gb|BW672395.1|BW672395
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|120493517|gb|EH221684.1|EH221684
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|22523580|gb|BU082391.1|BU082391
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|154204736|gb|EV554998.1|EV554998
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|16342969|gb|BI968564.1|BI968564
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|10231306|gb|BE800194.1|BE800194
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTGCGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|192295731|gb|FG990825.1|FG990825
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|120492558|gb|EH220725.1|EH220725
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|13480387|gb|BG509730.1|BG509730
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGAT
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGAT
EST: gi|192315106|gb|FK009930.1|FK009930
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|21676476|gb|BQ628827.1|BQ628827
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|117557747|gb|EG702132.1|EG702132
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
EST: gi|154204730|gb|EV554992.1|EV554992
EST:     AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAG                         GACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC
genomic: AGCCTTCCCAGCTCCTTGGCTCCGTGCTTCAAAGTTCTGGCCTACCACAGgtaatcatgt ... tgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtttgagaaagaaatgcatagactaattaataaatgtaacatgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGCCAGCATCACAGGCTGTTGAAGAACAAGCTGCTGCCACAGCATAGTGTGT
                     atagactaattaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaagaggtgctatgttgtatgtagtgggctagtggcttcataaatttgtttgagaaagaaatgcatagactaattaataaatgtaacatgtgtatcagGACGTGTTGATAATGTGTACGGTGACCGCAACCTGATTTGCACCCTTCTGCCAGCATCACAGGCTGTTGAAGAACAAGCTGCTGCCACAGCATAGTGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - -ggtgcta
- - - - - - - tgttgta
- - - - - - - - - - - gtagtgg
- - - - - - - - - - - - - - - - - tggcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa