RetrogeneDB ID: retro_cfam_677

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:18761777..18763074(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000005683
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cfam_677
ATGGCAGAACATGCAGCATTGGAGGAGCTAGTGCGACTTCAGGGAGAGCGCGTGCGGGGCCTCAAGCAGCAGAAGGCCAG
TGCTGAGCAGATCGAGGAGGAGGTGGCAAAACTACTGAAATTGAAGGCACAGCTGGGCCCTGATGAAGGGAAACAGAAGT
TTGTGCTCGAAACCCCAAGGGTACAAGAGCCTACAGTCCCCGGCAGATGGCCGTTGGAGAGAAGGTGTTTGATGTCATCA
TCAGCTGCTTCAAGCGTCATGGTACAGAAGTAATTGATACACCTGTGTCCGAACTAAAGGAAACACTAACTGGAAAGTAT
GGAGAAGACTCCAAGCTTATCTATGATCTGAAGGACCAGGGTGGAGAGCTATTGTCCCTTCGCTATGACCTCACTGTTCC
TTTTGCTCGATATTTGGCAATGAATGAACTGACCAACATTAAACGCTACCACATAGCCAAAGTGTATGGCGCGATAACCC
AGCCGTGACCCAAGGCCGGTATCGGGAATTCTATCAATGTGACTTTGACATTGCCGGACAATTTGACCCCATGATCCCTG
ATGCAGAGTGCCTGGAGATCATGTGTGAGATCCTGAGATCCCTTCAGATAGGCGACTTCCTGGTCAAGGTAAATGATAGG
CGCATCCTAGATGGGATGTTTGCCATCTGTGGTGCTCCTGATAGCAAGTTCCGTGCCATCTGCTCCTCAGGGAACAAGTT
GGACAAGGTGTCCTGGGAGGAAGTAAAGAATGAGATGGTGGGAGAGAAGGGCCTCGCACCCGAGGTAGCTGACCACATTG
GGGACTACGTCCAGCAGCATGGTGGGATATCCCTAGTGGAACAGCTGCTCCAGGATCCTGAACTGTCCCAAAACAAACAG
GCCTTGGAGGGCCTGGGAGACCTAAAACTACTGTTTGAATACCTGACCCTGTTTGGCATTGCTGACAAGATCACCTTCGA
CCTAAGCCTCGCTCGAGGGCTAGACTACTATACTGGGGTGATCTATGAGGCGGTGCTGCTACAAACCCCAGTGCAGGCAG
GGGAAGAGCCCCTGGGTGTGGGCAGTGTGGCTGCTGGAGGACGCTATGATGGGCTGGTGGGCATGTTCGACCCGAAAGGA
CGCAAGGTGCCATGCATGGGGCTTAGCATTGGGGTGGAGCGGATCTTTTCCATTGTGGAGCAGAGGCTAGAGGCTACGGA
GGAGAAAGTATGGACCACAGAGACACAAGTGCTTGTGGCATCTGCACAGAAAAAGCTGCTGGAGGAGAGACTAAAGCTTG
TCTCAGAGCTCTGGTCC

Alignment

ORF - retro_cfam_677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.4 %
• Parental protein coverage: 85.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAERAALEELVRLQGERVRGLKQQKASAEQIEEEVAKLLKLKAQLGPDEGKQKFVLKTP-KGTRDYSPRQ
          MAE.AALEELVRLQGERVRGLKQQKASAEQIEEEVAKLLKLKAQLGPDEGKQKFVL.TP.KGTR.YSPRQ
Retrocopy MAEHAALEELVRLQGERVRGLKQQKASAEQIEEEVAKLLKLKAQLGPDEGKQKFVLETP<KGTRAYSPRQ

Parental  MAVREKVFDVIISCFKRHGAEVIDTPVFELKETLTGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYL
          MAV.EKVFDVIISCFKRHG.EVIDTPV.ELKETLTGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYL
Retrocopy MAVGEKVFDVIISCFKRHGTEVIDTPVSELKETLTGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYL

Parental  AMNKLTNIKRYHIAKVYR-RDNPAMTRGRYREFYQCDFDIAGQFDPMIPDAECLEIMCEILRSLQIGDFL
          AMN.LTNIKRYHIAKVY..RDNPA.T.GRYREFYQCDFDIAGQFDPMIPDAECLEIMCEILRSLQIGDFL
Retrocopy AMNELTNIKRYHIAKVYG<RDNPAVTQGRYREFYQCDFDIAGQFDPMIPDAECLEIMCEILRSLQIGDFL

Parental  VKVNDRRILDGMFAICGVPDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADHIGDYVQQHGGIS
          VKVNDRRILDGMFAICG.PDSKFR.ICSS..KLDKVSWEEVKNEMVGEKGLAPEVADHIGDYVQQHGGIS
Retrocopy VKVNDRRILDGMFAICGAPDSKFRAICSSGNKLDKVSWEEVKNEMVGEKGLAPEVADHIGDYVQQHGGIS

Parental  LVEQLLQDPELSQNKQALEGLGDLKLLFEYLTLFGIADKISFDLSLARGLDYYTGVIYEAVLLQTPVQAG
          LVEQLLQDPELSQNKQALEGLGDLKLLFEYLTLFGIADKI.FDLSLARGLDYYTGVIYEAVLLQTPVQAG
Retrocopy LVEQLLQDPELSQNKQALEGLGDLKLLFEYLTLFGIADKITFDLSLARGLDYYTGVIYEAVLLQTPVQAG

Parental  EEPLGVGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEATEEKVRTTETQVLVASAQK
          EEPLGVGSVAAGGRYDGLVGMFDPKGRKVPC.GLSIGVERIFSIVEQRLEATEEKV.TTETQVLVASAQK
Retrocopy EEPLGVGSVAAGGRYDGLVGMFDPKGRKVPCMGLSIGVERIFSIVEQRLEATEEKVWTTETQVLVASAQK

Parental  KLLEERLKLVSELWN
          KLLEERLKLVSELW.
Retrocopy KLLEERLKLVSELWS

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	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_677 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_677 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 ,