Sequence
atgc intronic sequence ATGC exonic sequencegtatgcgccaatttaattatttatcttttagaatgaaatagtgaatgtaatcaataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
Basic information
species | Glycine max |
transcript | GLYMA08G42730.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 17
---------------------------gtatgcgccaatttaattat---ttatcttttagaatgaaatagtgaatgtaatcaataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
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gtaccaaactgtatcacttgtctctctatagtctcaagtctctttacaccctaaaccctgcgataaggttgtgatggagtatgctcttccatttga-acagGCTGAGAACATCAAGTTTACTTTGGAGCAGCAGATGGTGTTCTTTGCTCGATTAGTCGGGAATTTTAAGGTGGCAGATGATATAACTCCAATCAAGATCG
upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 17
---------gtatgcgccaatttaattatttatcttttagaatga--aatagtgaatgtaatcaataatgggt-tggat--gcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
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gtaaggcttttgatcacttgcattaataataacaagtcataaggattaacagtggattactttacttatatacattgattaacagGCGGAAAACATCAAATACACACTTGAGCAACAGATGGTGTTCTTTGCCCGAGTGGTTGGAGGGTTCAAAGTTGCTGATGACATCACTCCTTTGAAAATTG
upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 17
---------------gtatgcgccaatttaattatttatcttttagaatgaaatagtgaatgtaatcaataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
|| | | ||| || |||| | |||| || ||||| | | ||||||| | || || | ||||||| || ||||| || || | |||||||||||||| |||||||| || || || ||||||||||| || || ||||| |||| |||||||||||| |
gtatgtattatctatgttttatctaatcacataatttttatttttgaggtaaatattagaattaatcaa-attgtttt--acatagGCTGAAAATATTAAATTCACATTGGAGCAACAAATGGTATTCTTTGCTCGTTTAGTGGGACACTTCAAGGTGGCAGATGAGATTACTCCCATCAAAATCG
upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 17
-----------------gtatgcgccaatttaattatttatcttttagaatgaaatagtgaatgtaatca-ataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
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gtatttgcaatttctatgtttaatctaagcacgaaatttatatttatgagggaaacattagtactaatcagataacttttt--acacagGCTGAAAACATCAAGTTCACACTGGAGCAACAAATGGTGTTCTTTGCTCGTGTAGTGGGACACTTTGAAGTGGCGGATCAGATTACTCCAATCAAAATTGMapped 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|254323906|gb|GR836138.1|GR836138EST: TGCCAGTTGCTCTTGTTGAGTACGAAGGAGAACAACATGGTTTCCGGAAG GCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGA
genomic: TGCCAGTTGCTCTTGTTGAGTACGAAGGAGAACAACATGGTTTCCGGAAGgtatgcgcca ... ttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGA
EST:
gi|208261891|gb|GE058300.1|GE058300EST: TGCCAGTTGCTCTTGTTGAGTACGAAGGAGAACAACATGGTTTCCGGAAG GCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGA
genomic: TGCCAGTTGCTCTTGTTGAGTACGAAGGAGAACAACATGGTTTCCGGAAGgtatgcgcca ... ttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttatcttttagaatgaaatagtgaatgtaatcaataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
ttttagaatgaaata 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 |
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gtatgcgccaatttaattatttatcttttagaatgaaatagtgaatgtaatcaataatgggttggatgcagGCTGAGAACATTAAGTTTACTCTTGAGCAACAAATGGTCTTCTTTGCACGATTGGTTGGACACTTCAATGTTGCTGATGATATTAATCCCATCAAAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT