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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcctttgattttctccttctatatctgtcagataaatcccttacttccatccatgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG

Basic information

species Glycine max
transcript GLYMA08G26180.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 7
gtttgtgcctttgatt---ttctccttctatatctgtcagataaatcccttacttccatccatgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG
|| | |||     | |    | | | ||  | |   | |   | ||  || | ||    |||| |  | ||||  ||||| ||||| |||||| |||||||||| |||||||| | | ||||||||||||| ||||| || | ||||||  |  ||
gtatatgcaagcaaatgaactgttcatcctttttaattat-catattgctgattttagaccattt--tccagGCAACTGTTGCATATTATTTGCTATTGGACAATCGATTCCGAGCTACCAGTGGCTATCTGGGAGCAGACTATCAAGAATCATTG

upper sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 7
--------gtttgtgcctttgattttctc--cttctatatctg---tcagataaatcccttacttccatccatgtatt---tcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG
         ||  || || | ||  | |      |   | ||    ||  |||    |   | | ||||       ||    |||| ||||||  |||||||  |||||||||| ||||| ||||||||| | ||||||||||| | | | |||||||| ||||| |  
gtatgtagtttcctgtctctaatgcttttaatccccgaaactagtttccaatagtcactgaaatgccatttgctccttgtaccagGCTACTGTTACATACTACCTGTTATTGGATAACCGGTTCCGTGTTCCAAGTGGCTATCTAGAATCCGAGTTTCAGGAGACAACA

upper sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------------gtttgtgcctttgat---tttctccttctata-------------tctgtcaga------taaatcccttacttccatcca-tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG
                   |||| | |||| |   | | || ||  | |             ||  ||| |      ||||| |  || |   | | | ||| || ||||| |||||| | |||||| || || ||||||| || |||||||  || ||||| ||||| || |||||||||||||||||||||
gtatgtgtttcccacccacttgttcttttgctgtttctttcatttcaaagattaaaaaaaattccatcaaaagatcttaaatactgtattcttaccgactgtcttccagGGCACTGTGACGTACTATCTGATACTGGACAATCGTTTCCGTGCCTCTAGTGGTTATCTCGGGGCTGAGTTTCAAGAGACCATG

upper sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------gtttgtgcctttgattttct----------------ccttctatatctgtcagata--aatcccttacttccatccatgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG
                                    ||| |  | |  |  | |                 | |  ||||  | ||  ||     |  || | |||   | |  ||||||||| ||| || |||||||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||| ||  |  ||
gtataccattcctgacccttcaaactccttgtgtcttttctatcctccagatcccaaaaaaaaaaaaaaaacttattataattttccaattctgctttctgagttcttgcaaaatatttcagGCTACCGTTGCATACTATTTGCTATTGGACAACCGTTTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAGGAATCTTTG

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|9819566|gb|BE555079.1|BE555079
EST:     TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
genomic: TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
EST: gi|23734193|gb|BU765320.1|BU765320
EST:     TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
genomic: TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
EST: gi|193685389|gb|FK626605.1|FK626605
EST:     TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
genomic: TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
EST: gi|208265553|gb|GE063081.1|GE063081
EST:     TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
genomic: TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
EST: gi|209726301|gb|BW659614.1|BW659614
EST:     TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTA-TTGTTATTGGACAACCGATTCCGTGTTTCCAGT
genomic: TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
EST: gi|193644137|gb|FK592486.1|FK592486
EST:     GGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
genomic: GGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGT
EST: gi|17519479|gb|BM188521.1|BM188521
EST:     TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG                         GGTACTGTGGCATACTAT
genomic: TTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAGgtttgtgcct ... tgtatttcagGGTACTGTGGCATACTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctccttctatatctgtcagataaatcccttacttccatccatgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG
                             cccttac  putative branch site (score: 3)
        ttctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcctttgattttctccttctatatctgtcagataaatcccttacttccatccatgtatttcagGGTACTGTGGCATACTATTTGTTATTGGACAACCGATTCCGTGTTTCCAGTGGCTATCTTGGAGCTGAGTTTCAAGAGACCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA