RetrogeneDB ID: retro_cfam_1701

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:49156133..49157206(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017239
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHAX
• Ensembl ID: ENSCAFG00000000590
• Aliases: None
• Description: phosphorylated adaptor for RNA export [Source:HGNC Symbol;Acc:10241]

Sequence

>retro_cfam_1701
AAAACACTAGGTGGGGCCAGCACCGTGAGACCCTTCCAGGGTACTGCAACACCATGTGTACCGGTATCCCATTATCGAAC
TGTTAAAAGCGTGGATTCAAGTGAAGAGAGTTTTTCTGATTCAGATGATGATAGCTCCCTTTGGAAGCGCAAGCGACAGA
AATGTTTTAACCCTCCTCCAAAGCCAGAGCCTTTTCAGTTTGGCCAGAGCAGCCAGAAACCTCTTGTTCCTGGAGGAAAG
AAAGTTAACAATATATGGGGTGCTGTGCTACAAGAACAGAATCAAGATGCAGTGGCTACTGAACTTGGTATCTTGGGAAT
GGAGGGTACTATTGACAAAAGCAGACAATCTGAGACTTACAATTATTTGCTTGCTAAGAAACTTAAGAGGGAATCTCAAG
AACATACAAAGAGCTGGATGAATATATGCATGGTGGCAAAAAAATGGGATCAAAGGAAGAGGAAAATGGGCAAGGTCATC
TCAAACGGAAACGACCTGTCAAAGACAGACTAGGGGACAGACTAGAAATGAACTATAAAGGCCGCTATGAGATCACAGAG
GATGATGCGCAAGAGAAAGTGGCTGATGAAATTTCTTTCAGGTTGCAGGAACCAAAGAAAGATCTGATAGCACGAGTAGT
GAGGATAATTGGGAACAAAAAGGCGATTGAACTTCTGATGGAAACTGCTGAAGTTGAACAAAATGGTGGCCTTTTTATAA
TGAATGGTAGTCGAAGAAGAACACCAGGTGGAGTTTTCCTGAATCTCCTGAAAAATACTCCTAGTATTAGCGAGGAACAA
ATTAAGGACATTTTCTACATTGAAAATCAAAAGGAGTATGAAAATAAAAAGGCTGCTAGAAAGCGGAGAACACAAGTGTT
GGGAAAAAAGATGAAACAAGCTATTAAAAATCTAAATTTTCAAGAAGATGATGATACATCACGAGAAACTTTCGCGAGTG
ATATGAATGAGGCCCTGGTCTCTCTGGACGAGCCGCAGGAAGGCCACGGGGAGACAAAATTGGACCCAGAAGAAGCCATT
GAAGTTGATCATTCTAATGATTTGGACATCTTT

Alignment

ORF - retro_cfam_1701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.8 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTLGGDSTVRPFQGTATPCVPVSHYRTVKSVDSSEESFSDSDDDSSLWKRKRQKCFNPPPKPEPFQFGQS
          KTLGG.STVRPFQGTATPCVPVSHYRTVKSVDSSEESFSDSDDDSSLWKRKRQKCFNPPPKPEPFQFGQS
Retrocopy KTLGGASTVRPFQGTATPCVPVSHYRTVKSVDSSEESFSDSDDDSSLWKRKRQKCFNPPPKPEPFQFGQS

Parental  SQKPLVPGGKKVNNIWGAVLQEQNQDAVATELGILGMEGTIDKSRQSETYNYLLAKKLKRESQEHTK-EL
          SQKPLVPGGKKVNNIWGAVLQEQNQDAVATELGILGMEGTIDKSRQSETYNYLLAKKLKRESQEHTK.EL
Retrocopy SQKPLVPGGKKVNNIWGAVLQEQNQDAVATELGILGMEGTIDKSRQSETYNYLLAKKLKRESQEHTK<EL

Parental  DKELDEYMHGGKKMGSKEEENGQGHLKRKRPVKDRLGDRLEMNYKGRYEITEDDAQEKVADEISFRLQEP
          D....EYMHGGKKMGSKEEENGQGHLKRKRPVKDRLGDRLEMNYKGRYEITEDDAQEKVADEISFRLQEP
Retrocopy D----EYMHGGKKMGSKEEENGQGHLKRKRPVKDRLGDRLEMNYKGRYEITEDDAQEKVADEISFRLQEP

Parental  KKDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSISEEQIKDIFYIE
          KKDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSISEEQIKDIFYIE
Retrocopy KKDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSISEEQIKDIFYIE

Parental  NQKEYENKKAARKRRTQVLGKKMKQAIKNLNFQEDDDTSRETFASDTNEALASLDEPQEGHGETKLDPEE
          NQKEYENKKAARKRRTQVLGKKMKQAIKNLNFQEDDDTSRETFASD.NEAL.SLDEPQEGHGETKLDPEE
Retrocopy NQKEYENKKAARKRRTQVLGKKMKQAIKNLNFQEDDDTSRETFASDMNEALVSLDEPQEGHGETKLDPEE

Parental  AIEVDHSNDLDIF
          AIEVDHSNDLDIF
Retrocopy AIEVDHSNDLDIF

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	4.16 RPM	11.68 RPM
SRP017611_brain	3.02 RPM	8.26 RPM
SRP017611_kidney	3.76 RPM	9.97 RPM
SRP017611_liver	0.80 RPM	4.86 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1701 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010042	1 retrocopy	retro_amel_423,
Canis familiaris	ENSCAFG00000000590	2 retrocopies	retro_cfam_1136, retro_cfam_1701 ,
Myotis lucifugus	ENSMLUG00000000184	1 retrocopy	retro_mluc_1483,