RetrogeneDB ID: retro_cfam_977

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:10221401..10222581(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000001785
• Aliases: None
• Description: tRNA-splicing ligase RtcB homolog [Source:UniProtKB/TrEMBL;Acc:E2RCD6]

Sequence

>retro_cfam_977
ATGAGTCACAGGTATAATGATGAACTACAGTTCTTGGAAAAGATCAATAAAAACTGCTGAAGAATCAAGAAGGGCTTCAT
ACCCAACATGCAGGTGGAAGGCATTTTCTATGTGAATGACGCTTTGGAAAAATTAATGTTTGAGGAATTAAGAAATGCCT
GTCAAGGTGGTGGTGTTGGTGGCTTCCTACCAGCCAGGAAACAAATTGGCAATGTGGCAGCCCTGCCTGGGATTGTTCAT
AGATCTGTTGGGTTTCCTGATGTCCATTCAGATTATGGGTTTGCTATTGGGAATATGGCAGCCTTTGATATGAAAGACCC
CGATGCAGTGGTATCCCCAGGTGGTGTCAAATTTGACATCAACTGTGGTGTCCGCTTGCTAAGAACCTATTTGGATGAAA
GCGATGTCTAGCCTGTGAAGGAGCAGCTTGCCCAAGCTATGTTTGACTATATTCCTGTCGGAGTGAGTTCAAAAGGTGTC
ATCCCCATGAGTGCCAAAGACTTGGATGAGGCCTTGGAGATGGGTGTGGGTTGGTCCCTGAGGGAAGGCTATGCCTGGGC
TGAGAACAAGGAGCACTATGAGGAGTACGGCAGGATGTTGCAGGCCAACCCCAATAAGGTCTCTGCAAAGGCTAAGAAAA
GAGGCCTTCCTCAGTTAGGGACCCTGGGAGCAGGCAACCACTATGCAGAAATCCAAGTTGTGGATGAGATTTTCAATGAG
TATGCTGCTAAGAAAATGGGCATCGACCATAAGGGACAAGTATATGTGATGATCCACATTGGAAGCAGAGGCTTGGGCCA
CCAAGTAGCCACACTGGTAGCTATGGAAAAAGCCATGAAAAGAGACAAGATTATAGTCAACAACCATCAGTTAACTGGCT
TGTGCTTGGATTGCTTCCCCAGAGGGTCAGGACTACCTGCAGGGGATGGCAGCTGCTGGGAACTATGCCTGGGTCAACCA
CTCTTCCATGACCTTCCTAATCCATCAGGCCTTTGCCAAGGTCTTCAAAACAACCCCTGATGACTTGGACCTACGTGTGA
TCTACAACGTTTCTCACAATATTGCCAAAGTAGAACAGCATGTTGTGGACGGAAAGGAACGGACAGTGTTGGTACACAGG
AAGGGATCCACTTGAGCTTTCTCTCCTCACCATCCCCTCATTGCTGTGGATTACCAACTC

Alignment

ORF - retro_cfam_977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.64 %
• Parental protein coverage: 78.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRNACRGGGVGGFLPAMKQIG
          MS..YNDELQFLEKINKNC.RIKKGF.PNMQVEG.FYVNDALEKLMFEELRNAC.GGGVGGFLPA.KQIG
Retrocopy MSHRYNDELQFLEKINKNC*RIKKGFIPNMQVEGIFYVNDALEKLMFEELRNACQGGGVGGFLPARKQIG

Parental  NVAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVK
          NVAALPGIVHRS.G.PDVHS.YGFAIGNMAAFDM.DP.AVVSPGGV.FDINCGVRLLRT.LDESDV.PVK
Retrocopy NVAALPGIVHRSVGFPDVHSDYGFAIGNMAAFDMKDPDAVVSPGGVKFDINCGVRLLRTYLDESDV*PVK

Parental  EQLAQAMFDHIPVGVGSKGVIPMSAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQADPNKVSAR
          EQLAQAMFD.IPVGV.SKGVIPMSAKDL.EALEMGV.WSLREGYAWAE.KEH.EEYGRMLQA.PNKVSA.
Retrocopy EQLAQAMFDYIPVGVSSKGVIPMSAKDLDEALEMGVGWSLREGYAWAENKEHYEEYGRMLQANPNKVSAK

Parental  AKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKA
          AKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQV.VMIH.GSRGLGHQVAT..LVAMEKA
Retrocopy AKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVYVMIHIGSRGLGHQVAT--LVAMEKA

Parental  MKRDK-IIVNDRQ-LACARIASPEGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVI
          MKRDK.I..N....LACA.IASPEGQDYL.GMAAAGNYAWVN.SSMTFL..QAFAKVF.TTPDDLDL.VI
Retrocopy MKRDKIIVNNHQL>LACAWIASPEGQDYLQGMAAAGNYAWVNHSSMTFLIHQAFAKVFKTTPDDLDLRVI

Parental  YDVSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQL
          Y.VSHNIAKVEQHVVDGKERT.LVHRKGST.AF.PHHPLIAVDYQL
Retrocopy YNVSHNIAKVEQHVVDGKERTVLVHRKGST*AFSPHHPLIAVDYQL

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	52.62 RPM
SRP017611_brain	0.00 RPM	43.11 RPM
SRP017611_kidney	0.00 RPM	71.19 RPM
SRP017611_liver	0.00 RPM	24.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_977 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_977 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_977 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011070	1 retrocopy	retro_btau_1682,
Canis familiaris	ENSCAFG00000001785	2 retrocopies	retro_cfam_13, retro_cfam_977 ,
Myotis lucifugus	ENSMLUG00000007803	1 retrocopy	retro_mluc_1461,
Oryctolagus cuniculus	ENSOCUG00000008270	1 retrocopy	retro_ocun_1520,