RetrogeneDB ID: retro_cfam_298

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:26029763..26030858(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000011153
• Aliases: None
• Description: None

Sequence

>retro_cfam_298
GAAAAGGGAGTGTACATGACTGATATAACACCTCAAGGTGTGACTATGAAAGCTGGTGTCTTGGCAGGTGATCACTTGAT
TGAAGTGAATGAAGAGAATGTAGAAGATGCCAGCCATGAGGAAGTGGTTGCAAAGGTGAAGAACTCCGGAAATCATGTCA
TGTTCCTGTTGGTGGTCAAGGAGACTGACAAGCTCCATACTGAGCAGAAGATAGAATTGAAGAGAGAAACAGCCAGTCTG
AAACTGTTACCCCACCAGCCTCAGGTCGTAGAGATGAAGAAGGGAGGCAATGGATATGGTTTCTATCTGAGGGCAGGTCC
AGAACAGAAAGGTCAAGTCATCAAGGACATAGATTCTGGAAGTCCAGCAGAGGAGGCTGGCTTGAAGAACAATGACCTGC
TGGTGGCTGTCAATGGCGAGTCTGTGGAATCCCTGGATCATGACAGTGTGGTGGAAATGATTAGAAAGGGCGGAGATCAG
ACTTCGCTGCTGGTGGTAGACAAAGAGACAGACAACATGTACAGACTGGCTCATTTTTCTTCATTTCTCTACCATCAAAG
TCAAGAACTGCCTAATGGTTCTGTCAAGGAGGCTCCAGCTCCTACTCTTGCTCCTCCAGAGGTTTCAAGTTCAGATACTA
CAGAGGAAGTAGGAAATCATAAGCCTAAGCTCTGCAGGCTGGTTAAAGGCGAAAATGGCTATGGCTTCCACTTAAACGCG
ATTGAGGGTCAGCCAGGATCCTTCATCAAAGAGGTACAGAAGGGCAGCCCTGCTGAATTGGCAGGGTTGGAGGATGAAGA
TATCATCATTGAAGTGAATGGAGCGAAGGTGGTGGATGAACCCTATGAGAAGGTGGTAGACAGAATCCAGAGCAGTGGGA
AGAATGTCACACTCCTGGTCTGTGGAAAGAAGGCCTATGATTATTTCCAGGTTAAGAAAATCCCTGTTGTTTCCTCCATG
GCTGATCCACTGGATGAAACTCCTGATTCCAAAGAAGAAACACTGGCAGAACCAGAGCTCGAGTCACATGTGGCAAAAGA
ACGAGCTCACAGTACAGCCTCACATTCTTCTTCCAATTCTGAAGACACAGAGATG

Alignment

ORF - retro_cfam_298 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.89 %
• Parental protein coverage: 97.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKGVYMTDITPQGVAMKAGVLAGDHLIEVNGENVEDASHEEVVAKVKNSGSHVMFLLVDKETDKLHTEQK
          .KGVYMTDITPQGV.MKAGVLAGDHLIEVN.ENVEDASHEEVVAKVKNSG.HVMFLLV.KETDKLHTEQK
Retrocopy EKGVYMTDITPQGVTMKAGVLAGDHLIEVNEENVEDASHEEVVAKVKNSGNHVMFLLVVKETDKLHTEQK

Parental  IEFKRETASLKLLPRQPRVVEMKKGGNGYGFYLRAGPEQKGQVIKDIDSGSPAEEAGLKNNDLLVAVNGE
          IE.KRETASLKLLP.QP.VVEMKKGGNGYGFYLRAGPEQKGQVIKDIDSGSPAEEAGLKNNDLLVAVNGE
Retrocopy IELKRETASLKLLPHQPQVVEMKKGGNGYGFYLRAGPEQKGQVIKDIDSGSPAEEAGLKNNDLLVAVNGE

Parental  SVESLDYDSVVEMIRKGGDQTSLLVVDKETDNMYRLAHFSPFLYYQSQELPNGAVKQAPAPTLAPPEVSS
          SVESLD.DSVVEMIRKGGDQTSLLVVDKETDNMYRLAHFS.FLY.QSQELPNG.VK.APAPTLAPPEVSS
Retrocopy SVESLDHDSVVEMIRKGGDQTSLLVVDKETDNMYRLAHFSSFLYHQSQELPNGSVKEAPAPTLAPPEVSS

Parental  SDTTEEVGNHKPKLCRLVKGKNGYGFHLNAIQGQPGSFIKEVQKGSPAELAGLEDEDIIIEVNGAKVVDE
          SDTTEEVGNHKPKLCRLVKG.NGYGFHLNAI.GQPGSFIKEVQKGSPAELAGLEDEDIIIEVNGAKVVDE
Retrocopy SDTTEEVGNHKPKLCRLVKGENGYGFHLNAIEGQPGSFIKEVQKGSPAELAGLEDEDIIIEVNGAKVVDE

Parental  PYEKVVDRIQSSGKNVTLLVCGKKAYDYFQVKKIPVVSSMADPLDETPDSKEETLAEPELESHVAKERAH
          PYEKVVDRIQSSGKNVTLLVCGKKAYDYFQVKKIPVVSSMADPLDETPDSKEETLAEPELESHVAKERAH
Retrocopy PYEKVVDRIQSSGKNVTLLVCGKKAYDYFQVKKIPVVSSMADPLDETPDSKEETLAEPELESHVAKERAH

Parental  STASHSSSNSEDTEM
          STASHSSSNSEDTEM
Retrocopy STASHSSSNSEDTEM

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	3.11 RPM
SRP017611_brain	0.08 RPM	1.59 RPM
SRP017611_kidney	3.90 RPM	797.99 RPM
SRP017611_liver	0.29 RPM	50.76 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_298 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_298 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011153	1 retrocopy	retro_cfam_298 ,
Dasypus novemcinctus	ENSDNOG00000000375	2 retrocopies	retro_dnov_1158, retro_dnov_1857,
Myotis lucifugus	ENSMLUG00000028785	1 retrocopy	retro_mluc_1116,
Oryctolagus cuniculus	ENSOCUG00000024935	1 retrocopy	retro_ocun_133,