RetrogeneDB ID: retro_cfam_104

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:16856161..16858564(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002106
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000019273
• Aliases: None
• Description: None

Sequence

>retro_cfam_104
ATGGCGGCCCACCGTTCTGGCCCGCTCAAGCAGCAGAATAAAGCTCATAAAGGCGGACGGCATCGGGGTCGGGGATCCGC
GCAGCGGGACGGCAAGGGTCTGAAAATCTTAAGCAAGAAGGTGAGAAAAGAGCTCAGCAAAGTAGACCAGAGGCATCGCG
CTAGCCAGCTCCGAAAGCAGAAGAAAGAGGCGGTTCTGGCAGAGAAGAGACAGTTGGGCAGCAAGGATGGTCCTCCCCAT
CAGGTACTGGTGGTGCCCCTCCACGACAAGATTTCCCTGCCAGAGGCCTTTCGGTTGCTTCAGGATACAGACACCGGAAC
AGTACACTTGAATGAATGCGGAAGCACCCATAGCTTTATGTTGTTATGCCCTCGCTTGAAACATCGGTGGTTTTTCACAT
CTGCAAGGCCAGGGGATCTGCACACTGTGTTAGACATGGCCAAAGTGGCGGATACCATCCTTTTCCTCCTTGATCCACTA
GAAGGCTGGGACAGCATTGGGGATTACTGCCTTTCCTGCCTCTTTGCTCAGGGCCTTCCCACCTATACGCTAGCTGTCCA
GGGCATTTCTGGCCTCCCACCAAGGAAACAAATAGATGCCAGAAAGAAGCTAAGTAAAACAGTAGAGAAGCGTTTTCCTA
GTGACAAACTTCTTCTGTTAGACACTCAGCAGGAGGCAGAGATGCTGCTCAGGCAATTGGCCAACCAAAAGCAACGGCAT
CTTGCCTTTCGAGATCGACGGGCCTACCTGTTTGCTCACGCTGCTGACTTTGTGCCGAGTGAAGAAAATAACTTGGTGGG
CACCTTAAAAATCTCAGGCTATGTTCGTGGACAGACTCTAAATGTAAATAGCTTGCTGCATATCATTGGACAGGGTGATT
TCCAGATGAAACAGATAGATGCCCCTATGGACCCTTTCCCTTTAAATTTTAGAATGATCAAATCCCAAAAGGAGGACCCG
GGTGTGACAATGGAGATTTGTGCTATGGATGCTGTAGCTGATATGGAGGAAGACCTTAAGGTCGTAATGAAGGCAGACCC
TGATAAACAAGAATCTTTGCAAACAGAGGTTAACCTAGATCCAATGGAGGGGGAGCAGACCTGGCCCACAGAGGAGGAGC
TTAGTGAAGCAAATGACTTCTTGAAGGAAAGTTCCAAGGTGGTAAAGAAGGTTCCCAAAGGGACATCCAGTTACCAAGCT
GAATGGATTTTGGATGAGGATGGTGAAAGTGATGGGGAAGATGAATATGATGATATGCAACGTGAGGATTTTATTGAAGA
GGAATCTCAGGATGAGGGCAGTGAAAAGGAAGAGGAGGAGGAATATGAAACTATGACTATGGGAGAGTCTGTCCATGATG
ATCTATATGATGAGAATGTGGATGATGAGGCTGAGGAAAAAATGTTGGAGAAATATAAACAAGAAAGACTGCAAGAGATG
TTTCCAGATGAAATAGATACCCCCCGTGATGTGGCTGCAAGAATTAGATTTCAGAAATACAGAGGTCTCAAGAGCTTCCG
GACATCTCCGTGGGATCCTAAGGAAAACCTTCCTCAAGATTATGCTCGGATATTTCAATTTCAGAACTTTACTAATACTA
GGAAACGCATTTTTAAAGAAATTGAGGAAAAAGAAGTTGAAGGAGCTGAGGTTGGCTGGTATGTCACACTTCACGTCTCT
GAAGTTCCTCTCTCAGTGGTTGAGTACTTTAAGCGAGGAGCACCCTTGATTGCATTTTCTTTACTACCTCATGAACAGAA
GATGTCAGTACTAAATATGGTGGTGAGCCGGCACCCTGGCAACATTGAACCTGTGAAAGCCAAAGAGGATTTAATCTTCC
ACTGTGGGTTCAGGCGCTTCCGAGCCTCACCTTTATTCTCTCAGCACACTGCAGCGGATAAACATAAATTTCAGAGATTC
CTGACTGCTGATGTGGCCTTGGTGGTGACAATATATGGCCCAATCACGTTTCCTCCTGCATCTGTGCTGCTTTTCAAACA
GAATAGCAATGGCATGCACAGCCTCATTGCCACAGGCTATTTATTGTCAGTGGATCCAGACAGAATGGTCATCAAGAGAA
TTGTTTTGAGTGGTCATCCTTTCAAAATTTTTACTAAGATGGCAGTAGTGCGTTACATGTTCTTCAGCAGAGAGGATGTG
TTGTGGTTTAAACCCGTGGAACTGAGAACAAAGTGGGGCCGCAGGGGACACATCAAGGAACCTTTGGGTACTCATGGCCA
CATGAAGTGCAGTTTTGATGGGAAGCTAAAATCTCAGGACACAGTACTGATGAACCTCTATAAACGAGTTTTCCCCAAAT
GGACTTATGATCCATATGTACCAGACCCAGTACCATGGATGAAAAGTGAGATTTCTTTAGCAGTGCCTGAAGTGGACATG
GAG

Alignment

ORF - retro_cfam_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAHRSGPLKQQNKAHKGGRHRGRGSAQRDGKGEEIGLKILSKKVRKELSKVDQRHRASQLRKQKKEAVLA
          AAHRSGPLKQQNKAHKGGRHRGRGSAQRDGK....GLKILSKKVRKELSKVDQRHRASQLRKQKKEAVLA
Retrocopy AAHRSGPLKQQNKAHKGGRHRGRGSAQRDGK----GLKILSKKVRKELSKVDQRHRASQLRKQKKEAVLA

Parental  EKRQLGSKDGPPHQVLVVPLHDKISLPEAFRLLQDTDTGTVHLNECGSTHSFMLLCPRLKHRWFFTSARP
          EKRQLGSKDGPPHQVLVVPLHDKISLPEAFRLLQDTDTGTVHLNECGSTHSFMLLCPRLKHRWFFTSARP
Retrocopy EKRQLGSKDGPPHQVLVVPLHDKISLPEAFRLLQDTDTGTVHLNECGSTHSFMLLCPRLKHRWFFTSARP

Parental  GDLHTVLDMAKVADTILFLLDPLEGWDSIGDYCLSCLFAQGLPTYTLAVQGISGLPPRKQIDARKKLSKT
          GDLHTVLDMAKVADTILFLLDPLEGWDSIGDYCLSCLFAQGLPTYTLAVQGISGLPPRKQIDARKKLSKT
Retrocopy GDLHTVLDMAKVADTILFLLDPLEGWDSIGDYCLSCLFAQGLPTYTLAVQGISGLPPRKQIDARKKLSKT

Parental  VEKRFPSDKLLLLDTQQEAEMLLRQLANQKQRHLAFRDRRAYLFAHAADFVPSEENNLVGTLKISGYVRG
          VEKRFPSDKLLLLDTQQEAEMLLRQLANQKQRHLAFRDRRAYLFAHAADFVPSEENNLVGTLKISGYVRG
Retrocopy VEKRFPSDKLLLLDTQQEAEMLLRQLANQKQRHLAFRDRRAYLFAHAADFVPSEENNLVGTLKISGYVRG

Parental  QTLNVNSLLHIIGQGDFQMKQIDAPMDPFPLNFRMIKSQKEDPGVTMEICAMDAVADMEEDLKVVMKADP
          QTLNVNSLLHIIGQGDFQMKQIDAPMDPFPLNFRMIKSQKEDPGVTMEICAMDAVADMEEDLKVVMKADP
Retrocopy QTLNVNSLLHIIGQGDFQMKQIDAPMDPFPLNFRMIKSQKEDPGVTMEICAMDAVADMEEDLKVVMKADP

Parental  DKQESLQTEVNLDPMEGEQTWPTEEELSEANDFLKESSKVVKKVPKGTSSYQAEWILDEDGESDGEDEYD
          DKQESLQTEVNLDPMEGEQTWPTEEELSEANDFLKESSKVVKKVPKGTSSYQAEWILDEDGESDGEDEYD
Retrocopy DKQESLQTEVNLDPMEGEQTWPTEEELSEANDFLKESSKVVKKVPKGTSSYQAEWILDEDGESDGEDEYD

Parental  DMQREDFIEEESQDEGSEKEEEEEYETMTMGESVHDDLYDENVDDEAEEKMLEKYKQERLQEMFPDEIDT
          DMQREDFIEEESQDEGSEKEEEEEYETMTMGESVHDDLYDENVDDEAEEKMLEKYKQERLQEMFPDEIDT
Retrocopy DMQREDFIEEESQDEGSEKEEEEEYETMTMGESVHDDLYDENVDDEAEEKMLEKYKQERLQEMFPDEIDT

Parental  PRDVAARIRFQKYRGLKSFRTSPWDPKENLPRDYARIFQFQNFTNTRKRIFKEIEEKEVEGAEVGWYVTL
          PRDVAARIRFQKYRGLKSFRTSPWDPKENLP.DYARIFQFQNFTNTRKRIFKEIEEKEVEGAEVGWYVTL
Retrocopy PRDVAARIRFQKYRGLKSFRTSPWDPKENLPQDYARIFQFQNFTNTRKRIFKEIEEKEVEGAEVGWYVTL

Parental  HVSEVPLSVVEYFKRGAPLIAFSLLPHEQKMSVLNMVVSRHPGNIEPVKAKEDLIFHCGFRRFRASPLFS
          HVSEVPLSVVEYFKRGAPLIAFSLLPHEQKMSVLNMVVSRHPGNIEPVKAKEDLIFHCGFRRFRASPLFS
Retrocopy HVSEVPLSVVEYFKRGAPLIAFSLLPHEQKMSVLNMVVSRHPGNIEPVKAKEDLIFHCGFRRFRASPLFS

Parental  QHTAADKHKFQRFLTADVALVVTIYGPITFPPASVLLFKQNSNGMHSLIATGYLLSVDPDRMVIKRIVLS
          QHTAADKHKFQRFLTADVALVVTIYGPITFPPASVLLFKQNSNGMHSLIATGYLLSVDPDRMVIKRIVLS
Retrocopy QHTAADKHKFQRFLTADVALVVTIYGPITFPPASVLLFKQNSNGMHSLIATGYLLSVDPDRMVIKRIVLS

Parental  GHPFKIFTKMAVVRYMFFSREDVLW
          GHPFKIFTKMAVVRYMFFSREDVLW
Retrocopy GHPFKIFTKMAVVRYMFFSREDVLW

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	24.70 RPM
SRP017611_brain	1.03 RPM	22.23 RPM
SRP017611_kidney	1.12 RPM	13.74 RPM
SRP017611_liver	0.87 RPM	9.28 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_104 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_104 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
Canis familiaris	ENSCAFG00000019273	1 retrocopy	retro_cfam_104 ,
Cavia porcellus	ENSCPOG00000014833	2 retrocopies	retro_cpor_1258, retro_cpor_1307,
Oryctolagus cuniculus	ENSOCUG00000014256	1 retrocopy	retro_ocun_848,