RetrogeneDB ID: retro_cfam_151

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH374169.1:3567..5199(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000024588
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008879
• Aliases: None
• Description: None

Sequence

>retro_cfam_151
ATGATGCCCACACCAGTTATCCTGTTAAAAGAGGGGACCGATAGCTCCCAGGGCATCCCCCAGCTTGTAAGTAACATCAG
TGCCTGCCAAGTGATTGCGGAGGCTGTAAGAACCACCCTAGGCCCTCGTGGCATGGACAAGCTGATTGTAGATGGCCGAG
GCAAAGCAACAATTTCTAATGATGGGGCCACAATTCTGAAACTCCTTGATGTTGTCCATCCAGCAGCAAAGACTCTAGTG
GACATTGCTAAATCCCAAGACGCTGAGGTCGGTGATGGTACCACCTCAGTGACCCTGCTGGCTGCAGAGTTTCTGAAGCA
GGTGAAACCCTATGTGGAAGAAGGTTTGCACCCACAGATCATCATCCGAGCTTTCCGCACTGCCACCCAGTTGGCAGTTA
ACAAGATCAAAGAGATCGCTGTGACCGTGAAGAAGGAAGATAAAGTGGAACAGAGGAAGCTGCTGGAGAAGTGTGCCATG
ACCGCCCTGAGCTCTAAGCTGATTTCCCAGCAGAAAGCCTTCTTCGCTAAGATGGTGGTGGATGCAGTGATAATGCTCGA
TGAGTTGTTGCAGCTTAAAATGATTGGAATCAAGAAGGTGCAAGGTGGTGCTCTAGAGGAGTCCCAGCTGGTAGCTGGCG
TTGCATTCAAGAAGACTTTCTCTTATGCTGGGTTTGAAATGCAACCCAAAAAGTACAACAATCCAATGATTGCCCTTTTA
AATGTTGAGCTTGAGCTGAAAGCTGAGAAAGATAATGCTGAAATCAGAGTCCACACGGTGGAGGATTATCAGGCAATTGT
TGATGCTGAGTGGAACATTCTCTATGACAAGTTAGAGAGGATCCATCATTCTGGAGCCAAAGTCGTCTTATCCAAACTCC
CCATTGGGGATGTGGCCACCCAGTACTTTGCCGACAGGGACATGTTCTGTGCTGGCCGGGTGCCGGAGGAGGATCTGAAG
AGGACAATGATGGCCTGCGGAGGCTCCATCCAAACCAGTGTGAATGCTCTGTCAGCTGATGTGCTAGGCCGCTGCCAGGT
CTTTGAAGAGACGCAGATTGGAGGCGAGAGGTACAATTTCTTCACTGGCTGCCCCAAGGCCAAGACCTGCACTATCATCC
TTCGTGGTGGTGCTGAGCAGTTTATGGAGGAGACAGAGCGGTCTCTGCATGACGCCATCATGATCGTCAGGAGGGCCATC
AAGAATGATTCAGTGGTAGCTGGTGGCGGGGCCATTGAGATGGAGCTTTCCAAGTATCTGCGGGATTACTCAAGGACCAT
TCCAGGAAAACAGCAGCTGTTGATCGGGGCATATGCCAAGGCCTTGGAAATTATCCCACGTCAGCTGTGTGACAATGCTG
GCTTTGATGCCACAAACATCCTCAACAAGCTGCGGGCTCGGCATGCCCAGGGGGGCATGTGGTATGGAGTGGACGTCAAC
AATGAGGACATTGCTGACAACTTTGAGGCGTTTGTGTGGGAGCCAGCCATGGTGCGCATCAATGCCCTGACTGCAGCCTC
TGAGGCCGCCTGCCTTATCGTGTCAGTGGATGAGACCATCAAAAACCCTCGCTCAACAGTAGACGCTCCCCCAGCTGCGG
GCCGGGGACGGGGCCGGGGCCGCCCACACTGA

Alignment

ORF - retro_cfam_151 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  PTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVV
          PTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVV
Retrocopy PTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDVV

Parental  HPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNKIKEIAVT
          HPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNKIKEIAVT
Retrocopy HPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVNKIKEIAVT

Parental  VKKEDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVIMLDELLQLKMIGIKKVQGGALEESQLVA
          VKKEDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVIMLDELLQLKMIGIKKVQGGALEESQLVA
Retrocopy VKKEDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVIMLDELLQLKMIGIKKVQGGALEESQLVA

Parental  GVAFKKTFSYAGFEMQPKKYNNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLERIH
          GVAFKKTFSYAGFEMQPKKYNNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLERIH
Retrocopy GVAFKKTFSYAGFEMQPKKYNNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLERIH

Parental  HSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRCQVFEETQ
          HSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRCQVFEETQ
Retrocopy HSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRCQVFEETQ

Parental  IGGERYNFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYLRD
          IGGERYNFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYLRD
Retrocopy IGGERYNFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYLRD

Parental  YSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDVNNEDIADNFEAFV
          YSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDVNNEDIADNFEAFV
Retrocopy YSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGMWYGVDVNNEDIADNFEAFV

Parental  WEPAMVRINALTAASEAACLIVSVDETIKNPRSTVDAPPAAGRGRGRGRPH
          WEPAMVRINALTAASEAACLIVSVDETIKNPRSTVDAPPAAGRGRGRGRPH
Retrocopy WEPAMVRINALTAASEAACLIVSVDETIKNPRSTVDAPPAAGRGRGRGRPH

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	2.69 RPM	77.32 RPM
SRP017611_brain	3.81 RPM	30.17 RPM
SRP017611_kidney	7.26 RPM	47.48 RPM
SRP017611_liver	2.68 RPM	34.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_151 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_151 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151 ,
Choloepus hoffmanni	ENSCHOG00000007937	1 retrocopy	retro_chof_2313,
Cavia porcellus	ENSCPOG00000019869	1 retrocopy	retro_cpor_1458,
Echinops telfairi	ENSETEG00000009409	2 retrocopies	retro_etel_1478, retro_etel_607,
Homo sapiens	ENSG00000135624	1 retrocopy	retro_hsap_3354,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Nomascus leucogenys	ENSNLEG00000010414	1 retrocopy	retro_nleu_1175,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Pongo abelii	ENSPPYG00000012297	1 retrocopy	retro_pabe_2760,
Pan troglodytes	ENSPTRG00000012060	1 retrocopy	retro_ptro_2133,
Rattus norvegicus	ENSRNOG00000015630	2 retrocopies	retro_rnor_2179, retro_rnor_535,
Sorex araneus	ENSSARG00000011475	1 retrocopy	retro_sara_539,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,