RetrogeneDB ID: retro_cfam_2201

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:102555287..102556780(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HARS
• Ensembl ID: ENSCAFG00000005899
• Aliases: None
• Description: None

Sequence

>retro_cfam_2201
CGACTTCAGGGAGAGTGCGTGCAGGGCCTCAAGCAGCAGAAGGCCAGCACTGAGCAGATCGAGGAGGAGGTAGCAAAACT
ACTGAAATTGAAGGCGCAGCTGGGCCCTGATGAAAGGAAACAGAAGTTTGTGCTCAAAACCCCCAAGGGTACAAGAGACT
ACAGTCCCCAGCAGATGGCCGTTCGAGAGAAGGTGTTTGATGTAATCATCAGCTGCTTCAAGCGTCATGGTGCAGAAATA
ACTGATACACCTGTGTTCGAACTAAAGGAAACACTGACTGGAAAGTATGGAGAAGACTCTAAGCTTATCTATGATCTGAA
GGACCAGGGTGGAGAGCTATTGTCCCTTTGCTATGACCTCACTGTTCCTTTTGCTCGATATTTGGCAATGAATAAACTGA
CCAACATTAAACCCTACCACATAGCCAAAGTATATTGGTGCGATAACCCAGCCATGACCCGAGGCCAGTATCGGGAATTC
TATCAGTGTTACTTTGACATTGCCGGACAATTTGACCCCATGATCACTGATGCAGAGTGCCTGGAGATCATGAGTGAGAT
CCTGAGATCCCTTCAGATAGGCGACTTCCTGGTCAAGGTAAATGATAGGCACATCCTAGATGGGATGTTTGCCATCTGTT
GTGTTCCTGATAGCAAGTTCCGTACCATCTGCTCCTCAGTGGACAAGTTGGACAAGTGTCCTGGGAGGAAGTAAAGAATG
AGATGGTGGGAGAGAAGGGCCTCGCAACCAAAGTGCCCGACCACATTGGGGACTACATCCAGCAGCATGGTGGGATATCC
CTAGTGGAACAGCTGCTCCAGGATCCTGAACTGTCCCAAAACAAACAGGCCTTGGAGGGCCTGGGAGACCTAAAACTACT
GTTTGAATACTTGACCCTGTTTAGCATTGCTGACAAGATCTCCTTTGACCTAAGCCTCGTTTGAGGGCTAGACTAGTATA
CTGGGGTGATCTATGAGGCGGTGCTGCTACAAACCCCAGGGTAGGCAGGGGAAGAGCCCCTGGGTGTGGGCAATGTGGCT
GCTGAAGGACGCTATGATGGGCTGGTGGGCATGTTCGACCCTAAAGGATGCAAGGTGCCATGCGTGGGGCTCAGCATTGG
GGTGGAGCGGATCTTTTCCATTGTGGAGCAGAGGCTAGAGGCTACGGAGGAGAAAGTACGGACCACAGAGACACAAGTGC
TTGCGGCATCTGCACAGAAAAAGCTGCTGGAGGAGAGACTAAAGCTTGTCTCAGAGCTCTGGAATGCTGGGATCAAGGCA
GAGCTGCTCTATAAGAAGAACGCAAAGTTGCAGAACCAGTTGCAATACTGTGAGGAGGCAGGCATCCCACTGGTGGCCAT
CATTGGTGAGCAGGAGCTCAAAGATGGGGTCATCAAGCTCCGATCAGTGGCCAGCAGGGAAGAGGTGGACGTCCCAAGAG
AAGACCTTGTGGAAGAAATCAAAAGGAGAACAAGCCAGCCCCTTTGCATCTGC

Alignment

ORF - retro_cfam_2201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.99 %
• Parental protein coverage: 97.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLQGERVRGLKQQKASAEQIEEEVAKLLKLKAQLGPDEGKQKFVLKTPKGTRDYSPRQMAVREKVFDVII
          RLQGE.V.GLKQQKAS.EQIEEEVAKLLKLKAQLGPDE.KQKFVLKTPKGTRDYSP.QMAVREKVFDVII
Retrocopy RLQGECVQGLKQQKASTEQIEEEVAKLLKLKAQLGPDERKQKFVLKTPKGTRDYSPQQMAVREKVFDVII

Parental  SCFKRHGAEVIDTPVFELKETLTGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYH
          SCFKRHGAE..DTPVFELKETLTGKYGEDSKLIYDLKDQGGELLSL.YDLTVPFARYLAMNKLTNIK.YH
Retrocopy SCFKRHGAEITDTPVFELKETLTGKYGEDSKLIYDLKDQGGELLSLCYDLTVPFARYLAMNKLTNIKPYH

Parental  IAKVYRRDNPAMTRGRYREFYQCDFDIAGQFDPMIPDAECLEIMCEILRSLQIGDFLVKVNDRRILDGMF
          IAKVY..DNPAMTRG.YREFYQC.FDIAGQFDPMI.DAECLEIM.EILRSLQIGDFLVKVNDR.ILDGMF
Retrocopy IAKVYWCDNPAMTRGQYREFYQCYFDIAGQFDPMITDAECLEIMSEILRSLQIGDFLVKVNDRHILDGMF

Parental  AICGVPDSKFRTICSSVDKLDK-VSWEEVKNEMVGEKGLAPEVADHIGDYVQQHGGISLVEQLLQDPELS
          AIC.VPDSKFRTICSSVDKLDK.VSWEEVKNEMVGEKGLA..V.DHIGDY.QQHGGISLVEQLLQDPELS
Retrocopy AICCVPDSKFRTICSSVDKLDK<VSWEEVKNEMVGEKGLATKVPDHIGDYIQQHGGISLVEQLLQDPELS

Parental  QNKQALEGLGDLKLLFEYLTLFGIADKISFDLSLARGLDYYTGVIYEAVLLQTPVQAGEEPLGVGSVAAG
          QNKQALEGLGDLKLLFEYLTLF.IADKISFDLSL..GLD.YTGVIYEAVLLQTP..AGEEPLGVG.VAA.
Retrocopy QNKQALEGLGDLKLLFEYLTLFSIADKISFDLSLV*GLD*YTGVIYEAVLLQTPG*AGEEPLGVGNVAAE

Parental  GRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEATEEKVRTTETQVLVASAQKKLLEERLKLVSE
          GRYDGLVGMFDPKG.KVPCVGLSIGVERIFSIVEQRLEATEEKVRTTETQVL.ASAQKKLLEERLKLVSE
Retrocopy GRYDGLVGMFDPKGCKVPCVGLSIGVERIFSIVEQRLEATEEKVRTTETQVLAASAQKKLLEERLKLVSE

Parental  LWNAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVASREEVDVPREDLVEEIKR
          LWNAGIKAELLYKKN.KL.NQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVASREEVDVPREDLVEEIKR
Retrocopy LWNAGIKAELLYKKNAKLQNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVASREEVDVPREDLVEEIKR

Parental  RTSQPFCIC
          RTSQP.CIC
Retrocopy RTSQPLCIC

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	0.04 RPM	43.76 RPM
SRP017611_brain	0.00 RPM	61.85 RPM
SRP017611_kidney	0.00 RPM	27.87 RPM
SRP017611_liver	0.00 RPM	9.86 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2201 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2201 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005899	2 retrocopies	retro_cfam_2201 , retro_cfam_677,