RetrogeneDB ID: retro_cfam_141

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:50634404..50634812(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016577
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LGALS1
• Ensembl ID: ENSCAFG00000001487
• Aliases: None
• Description: Canis lupus familiaris galectin-1 (LGALS1), mRNA. [Source:RefSeq mRNA;Acc:NM_001201488]

Sequence

>retro_cfam_141
ATGGCTTGTGGTCTGGTCGCCAGCAATCTGAGTCTCAAACCTGGGCAGTGCCTCAGAGTGCAATGCGAGGTGGTCCCCGA
AGCCAAGAGCTTCGTGCTGAACCTGGGCAAAGACGGGGACAACCTGTGCCTGCACTTCAACCCTCGCTTTGAAGCCCACA
GCGACGTCAACACCATTGTGTGTAACAGCAAGGATGGCGGGGCCAGAGGCGAGGAGCATCGAGAGTCCGCCTTCCCCTTC
CAGCCCGGGACTGTCACAGAGGTGTGCATCTCCTTCGACCAGGCCGACTTGACCATCAAGCTGCCAGATGGATACACCTT
CAAGTTCCCCAACCGCCTCAACCTGGAGGCCATCAGCTACCTGGCAGCTGATGGTGACATGAAGATCAAGTGCCTGGCCT
TTGACTAA

Alignment

ORF - retro_cfam_141 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MACGLVASNLSLKPGQCLRVQCEVVPEAKSFVLNLGKDGDNLCLHFNPRFEAHGDVNTIVCNSKDGGAWG
          MACGLVASNLSLKPGQCLRVQCEVVPEAKSFVLNLGKDGDNLCLHFNPRFEAH.DVNTIVCNSKDGGA.G
Retrocopy MACGLVASNLSLKPGQCLRVQCEVVPEAKSFVLNLGKDGDNLCLHFNPRFEAHSDVNTIVCNSKDGGARG

Parental  EELRESAFPFQPGTVTEVCISFDQADLTIKLPDGYTFKFPNRLNLEAISYLAADGDMKIKCLAFD
          EE.RESAFPFQPGTVTEVCISFDQADLTIKLPDGYTFKFPNRLNLEAISYLAADGDMKIKCLAFD
Retrocopy EEHRESAFPFQPGTVTEVCISFDQADLTIKLPDGYTFKFPNRLNLEAISYLAADGDMKIKCLAFD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.63 RPM	40.86 RPM
SRP017611_brain	0.08 RPM	15.08 RPM
SRP017611_kidney	0.00 RPM	7.59 RPM
SRP017611_liver	0.00 RPM	3.92 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_141 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_141 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001487	1 retrocopy	retro_cfam_141 ,
Otolemur garnettii	ENSOGAG00000006935	5 retrocopies	retro_ogar_11, retro_ogar_1178, retro_ogar_2084, retro_ogar_467, retro_ogar_64,
Tursiops truncatus	ENSTTRG00000004798	1 retrocopy	retro_ttru_1501,