RetrogeneDB ID: retro_cfam_220

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:1157841..1159815(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006614
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000007840
• Aliases: None
• Description: None

Sequence

>retro_cfam_220
ATGAGGCTGAAGATTGGGTTCCTCTTACGCAGTCTGCTGGTGCTGGGAAGCTTCCTGGGGCTAGTGCTGCTCTGGTCTTC
CCTGTCCCCGCGCCCGGACGACCCGAGCCCGCTCAGCAGGATGAGGGAAGACAGAGATGTCAATAACCCCATGCCTAACC
GAGGAGGCGATGGATTAGCTCCTGGGGATGACAGATTCAAACCTGTTGTACCATGGCCTCATGTTGAAGGCGTAGAAGTG
GACTTAGAGTCTATTAGAAGAAAAAACAAGGCGAAAAATGAACAAGAGCGACATGCTGGTGGAGATAACCAGAAAGACAT
AATGCAGAGGCAGTATCTCACATTTAAGCCTCAAACATTCACCTACCGAGATCCTGTGCTACGTCCAGGGATCCTTGGTA
ACTTTGAACCCAAAGAACCTGAGCCTCACGGAGTGGTTGGTGGCCCTGGAGAGAACGCGAAGCCATTGGTTTTGGGACCA
GAATTCAAACATGCAATTCAAGCCAGCATTAAAGAGTTTGGATTTAACATGGTGGCAAGTGACATGATCTCACTGGACCG
CAGCGTCAATGACTTACGACAAGAAGAATGCAAGTATTGGCATTATGATGAAAACCTGCTGACTTCCAGTGTTGTCATCG
TCTTCCATAACGAAGGATGGTCAACCCTCATGAGAACAGTCCACAGTGTAATTAAAAGGACTCCGAGGAAATATTTAGCA
GAAATTGTGTTAATTGATGATTTCAGTAATAAAGAACACTTAAAAGAAAAACTAGATGACTACATTAAGCTGTGGAATGG
CTTGGTGAAGGTATTTCGAAATGAGAGAAGGGAAGGTCTGATTCAAGCACGAAGTATTGGTGCTCAGAAAGCCAAACTTG
GACAGGTTTTGATATACCTTGATGCCCACTGTGAGGTGGCGGTTAACTGGTATGCACCACTTGTAGCTCCCATATCTAAG
GACAGAACCATTTGCACTGTGCCGATTATAGATGTCATAAATGGCAACACATATGAAATTATACCCCAAGGGGGTGGTGA
TGAAGATGGGTATGCCCGAGGAGCATGGGATTGGAGTATGCTCTGGAAACGGGTGCCTCTGACCCCTCGAGAGAAGAGAA
TGAGAAAGACAAAAACTGAACCATATCGGTCCCCTGCCATGGCTGGTGGATTATTTGCCATTGAACGAGACTTCTTCTTT
GAACTGGGTCTGTATGATCCAGGTCTCCAGATTTGGGGTGGTGAAAACTTTGAGATCTCATATAAGATATGGCAGTGTGG
TGGCAAATTACTGTTTGTCCCTTGCTCTCGTGTTGGACACATCTACCGTCTTGAGGGTTGGCAAGGGAATCCTCCACCCA
TTTATGTTGGGTCTTCTCCAACTCTAAAGAATTATGTTAGAGTTGTAGAGGTTTGGTGGGATGAATATAAAGACTACTTC
TATGCTAGTCGTCCTGAATCAAAGGCATTACCATATGGAGATATATCTGAGCTGAAAAAATTTCGAGAAGATCACAACTG
CAAAAGTTTCAAATGGTTCATGGAAGAAATAGCTTATGATATAACTTCACACTACCCTCTACCTCCCAAAAATGTCGAAT
GGGGAGAAATCAGAGGGCTTGAGACTGTTTACTGCATTGACAGCATGGGGAAGACAAATGGAGGCTTTGTTGAACTAGGA
CCCTGCCACAGGATGGGAGGCAATCAGCTTTTTCGAATCAACGAAGCAAATCAACTCATGCAGTATGACCAGTGTTTAAC
AAAGGGGCCTGATGGATCAAAAATTATGATTACACACTGTAATCTAAATGAATTTAAGGAATGGCAGTACTTCAAGAGTC
TGCACAGATTTACTCACATTCCTTCAGGAAAGTGCTTAGATCGCTCAGATGTCCTACATCAAGTGTTCATCTCCAATTGC
GACTCCAGTAAAATGACTCAAAAGTGGGAAATGAACAACATCCATAGTGTTTAG

Alignment

ORF - retro_cfam_220 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PMPNRGGDGLAPGDDRFKPVVPWPHVEGVEVDLESIRRKNKAKNEQERHAGGDNQKDIMQRQYLTFKPQT
          PMPNRGGDGLAPGDDRFKPVVPWPHVEGVEVDLESIRRKNKAKNEQERHAGGDNQKDIMQRQYLTFKPQT
Retrocopy PMPNRGGDGLAPGDDRFKPVVPWPHVEGVEVDLESIRRKNKAKNEQERHAGGDNQKDIMQRQYLTFKPQT

Parental  FTYRDPVLRPGILGNFEPKEPEPHGVVGGPGENAKPLVLGPEFKHAIQASIKEFGFNMVASDMISLDRSV
          FTYRDPVLRPGILGNFEPKEPEPHGVVGGPGENAKPLVLGPEFKHAIQASIKEFGFNMVASDMISLDRSV
Retrocopy FTYRDPVLRPGILGNFEPKEPEPHGVVGGPGENAKPLVLGPEFKHAIQASIKEFGFNMVASDMISLDRSV

Parental  NDLRQEECKYWHYDENLLTSSVVIVFHNEGWSTLMRTVHSVIKRTPRKYLAEIVLIDDFSNKEHLKEKLD
          NDLRQEECKYWHYDENLLTSSVVIVFHNEGWSTLMRTVHSVIKRTPRKYLAEIVLIDDFSNKEHLKEKLD
Retrocopy NDLRQEECKYWHYDENLLTSSVVIVFHNEGWSTLMRTVHSVIKRTPRKYLAEIVLIDDFSNKEHLKEKLD

Parental  DYIKLWNGLVKVFRNERREGLIQARSIGAQKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRTTCTVPL
          DYIKLWNGLVKVFRNERREGLIQARSIGAQKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRT.CTVP.
Retrocopy DYIKLWNGLVKVFRNERREGLIQARSIGAQKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRTICTVPI

Parental  IDYIDGNDYSIEPQQGGDEDGFARGAWDWSLLWKRIPLSYKEKAKRKHKTEPYRSPAMAGGLFAIERDFF
          ID.I.GN.Y.I.PQ.GGDEDG.ARGAWDWS.LWKR.PL...EK..RK.KTEPYRSPAMAGGLFAIERDFF
Retrocopy IDVINGNTYEIIPQGGGDEDGYARGAWDWSMLWKRVPLTPREKRMRKTKTEPYRSPAMAGGLFAIERDFF

Parental  FELGLYDPGLQIWGGENFEISYKIWQCGGKLLFVPCSRVGHIYRLEGWQGNPPPIYVGSSPTLKNYVRVV
          FELGLYDPGLQIWGGENFEISYKIWQCGGKLLFVPCSRVGHIYRLEGWQGNPPPIYVGSSPTLKNYVRVV
Retrocopy FELGLYDPGLQIWGGENFEISYKIWQCGGKLLFVPCSRVGHIYRLEGWQGNPPPIYVGSSPTLKNYVRVV

Parental  EVWWDEYKDYFYASRPESKALPYGDISELKKFREDHNCKSFKWFMEEIAYDITSHYPLPPKNVEWGEIRG
          EVWWDEYKDYFYASRPESKALPYGDISELKKFREDHNCKSFKWFMEEIAYDITSHYPLPPKNVEWGEIRG
Retrocopy EVWWDEYKDYFYASRPESKALPYGDISELKKFREDHNCKSFKWFMEEIAYDITSHYPLPPKNVEWGEIRG

Parental  LETVYCIDSMGKTNGGFVELGPCHRMGGNQLFRINEANQLMQYDQCLTKGPDGSKIMITHCNLNEFKEWQ
          LETVYCIDSMGKTNGGFVELGPCHRMGGNQLFRINEANQLMQYDQCLTKGPDGSKIMITHCNLNEFKEWQ
Retrocopy LETVYCIDSMGKTNGGFVELGPCHRMGGNQLFRINEANQLMQYDQCLTKGPDGSKIMITHCNLNEFKEWQ

Parental  YFKSLHRFTHIPSGKCLDRSDVLHQVFISNCDSSKMTQKWEMNNIHSV
          YFKSLHRFTHIPSGKCLDRSDVLHQVFISNCDSSKMTQKWEMNNIHSV
Retrocopy YFKSLHRFTHIPSGKCLDRSDVLHQVFISNCDSSKMTQKWEMNNIHSV

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	2.10 RPM	2.48 RPM
SRP017611_brain	0.71 RPM	1.19 RPM
SRP017611_kidney	1.32 RPM	0.73 RPM
SRP017611_liver	0.87 RPM	0.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_220 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_220 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002494	1 retrocopy	retro_cfam_683,
Canis familiaris	ENSCAFG00000007840	1 retrocopy	retro_cfam_220 ,
Monodelphis domestica	ENSMODG00000025055	1 retrocopy	retro_mdom_1409,
Tupaia belangeri	ENSTBEG00000012122	1 retrocopy	retro_tbel_2374,