RetrogeneDB ID: retro_cfam_2018

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: AAEX03020959.1:26019..26670(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000014359
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LGALS3
• Ensembl ID: ENSCAFG00000015013
• Aliases: LGALS3, CBP 35, Gal-3, Galectin-3
• Description: Canis lupus familiaris lectin, galactoside-binding, soluble, 3 (LGALS3), mRNA. [Source:RefSeq mRNA;Acc:NM_001197043]

Sequence

>retro_cfam_2018
CCTCAAGGATGGCCTGGTCCATGGGGAAACCAGCCTGCTGGAGCAGGGGGATACTCAGGGGCCTCTTATCCTGGTGCCTA
CCCTGGCCAGGCACCTCCCGGCGGCTACCCTGGCCCCACAGCACCTGCTTATCCTGGCCCAACAGCACCAGGAGCCCAAC
CTGGGCAACCGAGTGGACCTGGGGCCTACCCGCCTCCTGGACAACCAAGCGCTTCGGGAACCTACCCTGCTGCTGGTCCC
TTTGGCATCCCTACTGGACCACTGACTGTGCCTTATGACCTGCCTTTGCCTGGAGGAGTCAAGCCTCGCATGCTGATAAC
AATTCTGGGCACAGTAAGGCCCAGTGAAAACAGACTTGCTTTAGATTTCAAGAGAGGGAATGATGTTGCCTTCCACTTTA
ACCCACGCTTCAATGAAGACAAGAGAGTCATTGTTTGCAATACCAAGCTGGATAATATCTGGGGAAAGGAAGAAAGGCAG
GCGGCTTTCCCATTTGAAAATGGTAAACCATTCAAAATACAAGTGCTGGTTGATTCTGACCACTTCAAGGTTGCGGTCAG
TGATGTCCATTTGTTGCAGTACAATCATCGTCTGAAAAATCTCCCAGAAATCAGCAAATTGGGTATTTCTGATGACATAG
ATCTCACCAGC

Alignment

ORF - retro_cfam_2018 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 74.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGGYPGQAPPGGYPGQAPPGGYPGQAPPGGYPGQAPPGTYPGPTAPAYPGPTAPGTQPGQPSGPGAYPPP
          P.G.PG..P.G..P..A..GGY.G...PG.YPGQAPPG.YPGPTAPAYPGPTAPG.QPGQPSGPGAYPPP
Retrocopy PQGWPG--PWGNQPAGA--GGYSGASYPGAYPGQAPPGGYPGPTAPAYPGPTAPGAQPGQPSGPGAYPPP

Parental  GQPSAPGAYPAAGPFGIPAGPLTVPYDLPLPGGVKPRMLITILGTVRPSANRLALDFKRGNDVAFHFNPR
          GQPSA.G.YPAAGPFGIP.GPLTVPYDLPLPGGVKPRMLITILGTVRPS.NRLALDFKRGNDVAFHFNPR
Retrocopy GQPSASGTYPAAGPFGIPTGPLTVPYDLPLPGGVKPRMLITILGTVRPSENRLALDFKRGNDVAFHFNPR

Parental  FNEDNKRVIVCNTKLDNIWGKEERQAAFPFESGKPFKIQVLVESDHFKVAVNDAHLLQYNHRMKNLPEIS
          FNED.KRVIVCNTKLDNIWGKEERQAAFPFE.GKPFKIQVLV.SDHFKVAV.D.HLLQYNHR.KNLPEIS
Retrocopy FNED-KRVIVCNTKLDNIWGKEERQAAFPFENGKPFKIQVLVDSDHFKVAVSDVHLLQYNHRLKNLPEIS

Parental  KLGISGDIDLTS
          KLGIS.DIDLTS
Retrocopy KLGISDDIDLTS

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	0.13 RPM	6.85 RPM
SRP017611_brain	0.32 RPM	7.38 RPM
SRP017611_kidney	1.19 RPM	45.10 RPM
SRP017611_liver	0.00 RPM	1.38 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2018 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2018 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015013	1 retrocopy	retro_cfam_2018 ,
Canis familiaris	ENSCAFG00000024191	1 retrocopy	retro_cfam_597,
Mustela putorius furo	ENSMPUG00000005725	2 retrocopies	retro_mputfur_115, retro_mputfur_535,
Pteropus vampyrus	ENSPVAG00000016067	1 retrocopy	retro_pvam_103,
Tarsius syrichta	ENSTSYG00000009020	4 retrocopies	retro_tsyr_1233, retro_tsyr_1390, retro_tsyr_1784, retro_tsyr_625,