RetrogeneDB ID: retro_cfam_2069

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:42472979..42474053(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015941
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLDIP2
• Ensembl ID: ENSCAFG00000018665
• Aliases: None
• Description: None

Sequence

>retro_cfam_2069
CGGGCTGCGTGGCCCGGCGGGCCCTGGCCGTGGGCAGCCGCTGGTGGGCCGAGGCCACTCTGTGTGGCAGGTGGAGCTGG
GGCCTTCCTGCCAGCGGCGACAGCGACGACGCGGAGGCACCTCTCGTCCCGAAACCGACCAGAGGGCAAAGTTTTGGAGA
CGGTTGGTGTATTTGAGGTGCCAAAACAGAATGGAAAATATGAGACCGGGCAGCTCTTTCTTCATAGTGTTTTTGGCTAC
CGAGGTGTCATCCTGTTTCCCTGGCAGGCCAGACTATATGACCGGGATGTGGCTTCTGCAGCTCCAGAGAAAGCAGAGAA
TCCTGCTGGCCATGGCTCTAAGGAGGTGAAAGGCAAAACTCACACTTACTATCAGGTGCTGATTGATGCCCGAGACTGTC
CACATATATCTCAGAGATCTCAGACAGAAGCTGTGACTTTCTTGGCTAACCATGATGACAGCCGGGCCCTTTACGCCATC
CCAGGCCTGGACTATGTCAGCCGCGAAGACATCCTCCCCTATACCTCTACCGATCAGGTTCCCATCCAGCATGAGCTGTT
TGAAAGATTTCTTCTGTATGACCAGACAAAAGCACCCCCTTTTGTGGCCCAGGAGACGCTACGGGCCTGGCAAGAGAAGA
ACCACCCCTGGCTGGAGCTCTCTGATGTTCACCGGGAGACAACAGAGAACATTCGTGTCACTGTCATCCCCTTCTACATG
GGCATGAGGGAAGCCCAGAATTCCCATGTCTACTGGTGGCACTACTGTATCCGCTTAGAGAACCTCGATAGTGATGTGGT
GCAGCTCCGGGAGCGACACTGGAGGATATTCAGTTTATCTGGCACCTTGGAGACAATGAGAGGCCGAGGGGTGGTGGGCA
GGGAACCAGTGTTATCCAAGGAGCAGCCCGCATTCCAGTTCAGCAGCCACGTCTCCCTGCAAGCTTCCAGCGGGTACATG
TGGGGCACATTCCGCTTTGAGAGGCCTGATGGCTCCCACTTTGATGTTCGGATCCCTCCCTTCTCCCTGGAAAGCAATAA
AGATGAGAAAACACCACCTTCAGGCCTTCACTGG

Alignment

ORF - retro_cfam_2069 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.2 %
• Parental protein coverage: 98.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RALAVGSRW-WARSLTGARGPRPLCVAGGAGAFPPAAAATTRRHLSSRNRPEGKVLETVGVFEVPKQNGK
          RA...G..W.WA.....A.GPRPLCVAGGAGAF.PAA.ATTRRHLSSRNRPEGKVLETVGVFEVPKQNGK
Retrocopy RAAWPGGPWPWA----AAGGPRPLCVAGGAGAFLPAATATTRRHLSSRNRPEGKVLETVGVFEVPKQNGK

Parental  YETGQLFLHSVFGYRGVVLFPWQARLYDRDVASAAPEKAENPAGHGSKEVKGKTHTYYQVLIDARDCPHI
          YETGQLFLHSVFGYRGV.LFPWQARLYDRDVASAAPEKAENPAGHGSKEVKGKTHTYYQVLIDARDCPHI
Retrocopy YETGQLFLHSVFGYRGVILFPWQARLYDRDVASAAPEKAENPAGHGSKEVKGKTHTYYQVLIDARDCPHI

Parental  SQRSQTEAVTFLANHDDSRALYAIPGLDYVSHEDILPYTSTDQVPIQHELFERFLLYDQTKAPPFVARET
          SQRSQTEAVTFLANHDDSRALYAIPGLDYVS.EDILPYTSTDQVPIQHELFERFLLYDQTKAPPFVA.ET
Retrocopy SQRSQTEAVTFLANHDDSRALYAIPGLDYVSREDILPYTSTDQVPIQHELFERFLLYDQTKAPPFVAQET

Parental  LRAWQEKNHPWLELSDVHRETTENIRVTVIPFYMGMREAQNSHVYWWRYCIRLENLDSDVVQLRERHWRI
          LRAWQEKNHPWLELSDVHRETTENIRVTVIPFYMGMREAQNSHVYWW.YCIRLENLDSDVVQLRERHWRI
Retrocopy LRAWQEKNHPWLELSDVHRETTENIRVTVIPFYMGMREAQNSHVYWWHYCIRLENLDSDVVQLRERHWRI

Parental  FSLSGTLETVRGRGVVGREPVLSKEQPAFQYSSHVSLQASSGHMWGTFRFERPDGSHFDVRIPPFSLESN
          FSLSGTLET.RGRGVVGREPVLSKEQPAFQ.SSHVSLQASSG.MWGTFRFERPDGSHFDVRIPPFSLESN
Retrocopy FSLSGTLETMRGRGVVGREPVLSKEQPAFQFSSHVSLQASSGYMWGTFRFERPDGSHFDVRIPPFSLESN

Parental  KDEKTPPSGLHW
          KDEKTPPSGLHW
Retrocopy KDEKTPPSGLHW

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	48.63 RPM
SRP017611_brain	0.32 RPM	40.57 RPM
SRP017611_kidney	0.46 RPM	59.57 RPM
SRP017611_liver	0.73 RPM	32.41 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2069 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018665	1 retrocopy	retro_cfam_2069 ,
Callithrix jacchus	ENSCJAG00000012566	1 retrocopy	retro_cjac_1445,
Oryctolagus cuniculus	ENSOCUG00000007781	1 retrocopy	retro_ocun_1169,