RetrogeneDB ID: retro_cfam_1929

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:2385248..2386092(-)
• Located in intron of: ENSCAFG00000031023

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000000172
• Aliases: None
• Description: mRNA cap guanine-N7 methyltransferase [Source:UniProtKB/TrEMBL;Acc:E2R4R3]

Sequence

>retro_cfam_1929
CGCGATAACACTGTTTTGGACCTGGGATGGGGTAAAGGTGGAGATTTGCTCAAATGGAAAAAGGGAAGAATTAACAAGCT
AGTTTGTACAGATATCGCTGATGTTTCAGTCAAACAGTGTCAGCAGTGGTATGTAGACATGAAAAATCGTTGTCGTGATA
ATGAATATATTTTCAGTGCAGAATTTGTAACTGCTGATTGTTCAAAGGAACTTTTGATTAACAAATTTCGTGATGCCGAA
ACATGCTTTGACATCTGTAGTTGTCAGTTTGTCTGTCATTATTCATTTGAATCCTATGAGCAGGCTGACATGATGCTCAG
AAATGCCTGTGAGAGACTGAGCCCTGGAGGCTATTTTATTGGTACCACTCCCAATAGCTTTGAACTGATAAGACGCCTTG
AAGCTTCAGAAACAGAATCATTTGGGAATGAGATATATACTGTGAAGTTTCAGAAGGAAGGAGATTATCCTTTATTTGGC
TGCAAATGTGACTTCAACTTGGAAGGTGTTGTGGATGTCCCTGAATTCCTGGTCTATTTTCCATTGCTAAATGAAATGGC
AAAGAAGTACAATATGAAACTAGTCTACAAAAAGACATTTCTGGAATTCTATGAGGAAAAGATTAAGCACAACGAAAATA
AAATGCTGTTAAAACGAATGCAGGCCTTGGAGCCATATCCAGCAAATGAGAATTCCAAACTGCCTCTCCGAGAAGGTGGA
TGACTATGAACATGTAGCAGAGTACATGAAGAACAGTCAAGTAAGGTTACCTTGGGGAACCTTAAGTAAATCAGAGTGGG
AAGCCACAAGCATTTACTTGGTTTTTGCATTTGAGAAGCAGCAG

Alignment

ORF - retro_cfam_1929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.04 %
• Parental protein coverage: 58.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRCRDNEYIFNAEFVTADCSKE
          RD.TVLDLG.GKGGDLLKWKKGRINKLVCTDIADVSVKQCQQ.Y.DMKNRCRDNEYIF.AEFVTADCSKE
Retrocopy RDNTVLDLGWGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQWYVDMKNRCRDNEYIFSAEFVTADCSKE

Parental  LLFNKFRDPETCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETES
          LL.NKFRD.ETCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETES
Retrocopy LLINKFRDAETCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETES

Parental  FGNEIYTVKFQKKGDYPLFGCKYDFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKN
          FGNEIYTVKFQK.GDYPLFGCK.DFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIK.
Retrocopy FGNEIYTVKFQKEGDYPLFGCKCDFNLEGVVDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKH

Parental  NENKMLLKRMQALEPYPANENSKL-ASEKVDDYEHAAEYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEK
          NENKMLLKRMQALEPYPANENSKL..SEKVDDYEH.AEYMKNSQVRLP.GTLSKSEWEATSIYLVFAFEK
Retrocopy NENKMLLKRMQALEPYPANENSKL>LSEKVDDYEHVAEYMKNSQVRLPWGTLSKSEWEATSIYLVFAFEK

Parental  QQ
          QQ
Retrocopy QQ

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	0.00 RPM	20.75 RPM
SRP017611_brain	0.00 RPM	16.12 RPM
SRP017611_kidney	0.07 RPM	9.25 RPM
SRP017611_liver	0.00 RPM	5.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1929 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000172	1 retrocopy	retro_cfam_1929 ,
Cavia porcellus	ENSCPOG00000011388	1 retrocopy	retro_cpor_442,
Monodelphis domestica	ENSMODG00000021415	1 retrocopy	retro_mdom_1781,
Tupaia belangeri	ENSTBEG00000005594	1 retrocopy	retro_tbel_4062,