RetrogeneDB ID: retro_cfam_558

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:61866223..61867198(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002959
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AKR1A1
• Ensembl ID: ENSCAFG00000004549
• Aliases: None
• Description: Canis lupus familiaris aldo-keto reductase family 1, member A1 (aldehyde reductase) (AKR1A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252168]

Sequence

>retro_cfam_558
ATGGCGGCTTCATGTGTCCTCCTGCACACTGGGCAGAAGATGCCCCTGATTGGGCTGGGCACCTGGAAGAGTGATCCTGG
CCAGGTAAAAGCAGCTATTATGTATGCCCTGAGTGTAGGCTACCGCCACATTGACTGTGCTGCTATCTACGGCAATGAGG
CTGAGATCGGGGAGGCCCTGAAGGAGAATGTAGGACCTGGCAAGGTGGTGCTTCGAGAGGAGCTGTTTGTGACTTCTAAG
CTGTGGAACACTAAACACCACCCCAAGGATGTGGAGCCTGCCCTCCGGAAGACACTGGCTGACCTCCAGCTGGAGTATTT
GGACCTGTACCTGATGCACTGGCCTTATGCCTTTGAGCGGGGAGACAACCCTTTCCCTAAAAATGCCGATGGGACAGTCC
GCTATGACTCTACCCACTACAAGGAGACCTGGAAAGCTCTGGAGGCACTGGTGGCTAAGGGACTGGTACGAGCACTGGGC
CTGTCCAATTTCAGCAGTCGGCAGATCGATGATGTGCTCAGTGTGGCCTCTGTACGCCCAGCTGTCCTGCAGGTGGAATG
TCACCCATACTTGGCTCAGAAGGAGCTGATTGCTCATTGCCAAGCACGCGGCCTGGAGGTGACCGCTTATAGCCCTCTGG
GATCCTCTGATAGAGCTTGGCGTGATCCTGATGAGCCTGTCCTACTTGAGGAGCCGGTAGTCTTGGCACTGGCTGAAAAG
TATGGCCGGTCTCCAGCTCAGATCCTGCTCAGGTGGCAGGTCCAGCGGAAAGTGATCTGCATCCCCAAGAGTATCACACC
TTCACGTATTCTCCAGAACATACAGGTGTTTGACTTCACCTTTAGCCCAGACGAGATGAAGCAGCTAGATGCCCTGAATA
AAAATTGGCAATACATTGTGCCCATGCTCACAGTGGATGGGAAGAGGGTCCCGAGAGATGCAGGGCACCCTCTGTACCCC
TTTAATGATCCATAC

Alignment

ORF - retro_cfam_558 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASCVLLHTGQKMPLIGLGTWKSDPGQVKAAIMYALSVGYRHIDCAAIYGNEAEIGEALKENVGPGKVV
          MAASCVLLHTGQKMPLIGLGTWKSDPGQVKAAIMYALSVGYRHIDCAAIYGNEAEIGEALKENVGPGKVV
Retrocopy MAASCVLLHTGQKMPLIGLGTWKSDPGQVKAAIMYALSVGYRHIDCAAIYGNEAEIGEALKENVGPGKVV

Parental  LREELFVTSKLWNTKHHPKDVEPALRKTLADLQLEYLDLYLMHWPYAFERGDNPFPKNADGTIRYDSTHY
          LREELFVTSKLWNTKHHPKDVEPALRKTLADLQLEYLDLYLMHWPYAFERGDNPFPKNADGT.RYDSTHY
Retrocopy LREELFVTSKLWNTKHHPKDVEPALRKTLADLQLEYLDLYLMHWPYAFERGDNPFPKNADGTVRYDSTHY

Parental  KETWKALEALVAKGLVRALGLSNFSSRQIDDVLSVASVRPAVLQVECHPYLAQKELIAHCQARGLEVTAY
          KETWKALEALVAKGLVRALGLSNFSSRQIDDVLSVASVRPAVLQVECHPYLAQKELIAHCQARGLEVTAY
Retrocopy KETWKALEALVAKGLVRALGLSNFSSRQIDDVLSVASVRPAVLQVECHPYLAQKELIAHCQARGLEVTAY

Parental  SPLGSSDRAWRDPDEPVLLEEPVVLALAEKYGRSPAQILLRWQVQRKVICIPKSITPSRILQNIQVFDFT
          SPLGSSDRAWRDPDEPVLLEEPVVLALAEKYGRSPAQILLRWQVQRKVICIPKSITPSRILQNIQVFDFT
Retrocopy SPLGSSDRAWRDPDEPVLLEEPVVLALAEKYGRSPAQILLRWQVQRKVICIPKSITPSRILQNIQVFDFT

Parental  FSPDEMKQLDALNKNWRYIVPMLTVDGKRVPRDAGHPLYPFNDPY
          FSPDEMKQLDALNKNW.YIVPMLTVDGKRVPRDAGHPLYPFNDPY
Retrocopy FSPDEMKQLDALNKNWQYIVPMLTVDGKRVPRDAGHPLYPFNDPY

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	28.18 RPM
SRP017611_brain	0.24 RPM	19.93 RPM
SRP017611_kidney	4.75 RPM	305.42 RPM
SRP017611_liver	0.65 RPM	34.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_558 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001290	1 retrocopy	retro_cfam_63,
Canis familiaris	ENSCAFG00000004549	1 retrocopy	retro_cfam_558 ,
Callithrix jacchus	ENSCJAG00000013633	2 retrocopies	retro_cjac_3093, retro_cjac_3334,
Echinops telfairi	ENSETEG00000006450	1 retrocopy	retro_etel_1106,
Macropus eugenii	ENSMEUG00000007370	1 retrocopy	retro_meug_1,
Otolemur garnettii	ENSOGAG00000007175	2 retrocopies	retro_ogar_1522, retro_ogar_2582,
Tarsius syrichta	ENSTSYG00000005301	1 retrocopy	retro_tsyr_1409,
Tursiops truncatus	ENSTTRG00000012180	1 retrocopy	retro_ttru_751,