RetrogeneDB ID: retro_cfam_875

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:30057549..30058014(-)
• Located in intron of: ENSCAFG00000004855

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TXNL1
• Ensembl ID: ENSCAFG00000000137
• Aliases: None
• Description: thioredoxin-like 1 [Source:HGNC Symbol;Acc:12436]

Sequence

>retro_cfam_875
GGCATCAAATGCCTTAATGAAAGTGATGAGCATGGATTTGACAACTGTTTACGAAAAGATATGACCTTGGAATCTGATTG
TGATGAACAGCTACTTATTACTGTGGCATTTAATCAGCCTGTTAAGCTTTATTCAATGAAATTTCAAGGGCCTAATAATG
GTCAGGGTCCTAAATATGTAAAAATTTTTATCAATCTACCCCGAACTATGGATTTTGAAGAAGCAGAAAGAAGTGAACCA
ACTCAAGCTCTGGAACTAACAGAGGATGATATTAAAGAAGATGGCATTGTCCCACTTCGTTATGTTAAGTTTCAGAATGT
TAACAGTGTAACTATATTTGTTCAGTCCAATCAAGGTGAAGAAGAAACAACAAGAATTTCATATTTTACTTTTATTGGTA
CTCCAGTCCAGGCAACCAATATGAATGACTTCAAACGAGTAGTTGGCAAAAAATGAGAAAGCCAC

Alignment

ORF - retro_cfam_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.15 %
• Parental protein coverage: 53.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCECLNESDEHGFDNCLRKDMTFLESDCDEQLLITVAFNQPVKLYSMKFQGPDNGQGPKYVKIFINLPRS
          G..CLNESDEHGFDNCLRKDMT.LESDCDEQLLITVAFNQPVKLYSMKFQGP.NGQGPKYVKIFINLPR.
Retrocopy GIKCLNESDEHGFDNCLRKDMT-LESDCDEQLLITVAFNQPVKLYSMKFQGPNNGQGPKYVKIFINLPRT

Parental  MDFEEAERSEPTQALELTEDDIKEDGIVPLRYVKFQNVNSVTIFVQSNQGEEETTRISYFTFIGTPVQAT
          MDFEEAERSEPTQALELTEDDIKEDGIVPLRYVKFQNVNSVTIFVQSNQGEEETTRISYFTFIGTPVQAT
Retrocopy MDFEEAERSEPTQALELTEDDIKEDGIVPLRYVKFQNVNSVTIFVQSNQGEEETTRISYFTFIGTPVQAT

Parental  NMNDFKRVVGKKGESH
          NMNDFKRVVGKK.ESH
Retrocopy NMNDFKRVVGKK*ESH

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	0.04 RPM	37.50 RPM
SRP017611_brain	0.00 RPM	34.46 RPM
SRP017611_kidney	0.13 RPM	86.24 RPM
SRP017611_liver	0.22 RPM	36.47 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_875 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_875 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000137	1 retrocopy	retro_cfam_875 ,
Choloepus hoffmanni	ENSCHOG00000010262	1 retrocopy	retro_chof_1723,
Ictidomys tridecemlineatus	ENSSTOG00000000075	2 retrocopies	retro_itri_302, retro_itri_414,
Tupaia belangeri	ENSTBEG00000017328	2 retrocopies	retro_tbel_1981, retro_tbel_911,
Tursiops truncatus	ENSTTRG00000001161	1 retrocopy	retro_ttru_1154,