RetrogeneDB ID: retro_cfam_1389

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:76439700..76440541(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS6
• Ensembl ID: ENSCAFG00000014814
• Aliases: None
• Description: COP9 signalosome subunit 6 [Source:HGNC Symbol;Acc:21749]

Sequence

>retro_cfam_1389
CTCTTCATCCTCAATATTTCAGACCATTGGATTTGCATGTGCTCCCAAGAGGGGTGGCCTATGCAGGTGATTGGGGCACT
GATTGGGAAGCAGGAGGGCAGAAATATCGAGGTGATGAACTCCTTTGAGCTGCTGTCCCACACCGTGGAGCAGAAGATCA
TCATTGACAAAGAGTATTACTACACCAGGGAGGAGCAATTCAAACAGGTGTTCAAGGAGCTGGAGTGTTGGGGTTGGTAT
ACCACCGGGAGGCCGCCTGACCCCTTGGACATCCAAGTCCACAAGCAGGTGTGGAGATCACTGAGAGCCTACTCTTCTTA
AGTTGAATCCTATGACCAAGGACACAGATCTTCCCATCAGTGTTTTTGAGTCTGTCATCGATATAATCAATGGAGAGCCA
CAATGTTATTTGCAGAACTGACCTACACTCTGGCCACAGAGGAAGCCGAAGGCATTGGTGTCAAACCCATGGCCTGAATG
ACGGCCACAGGCAGCGGTGAGAACTCCACATGGCTGAACACCTGATAGTGCAACACAGGACCATCAAGATGCTGTGCAGC
CGGGTCAAGCTCATCTTGGAATACGTCAAGGCCTCTGAAGCCTGAGAGGTCCCCTTTAACCATGAGATCTGCGGGAGCCC
TATGCTCTGTGTCACTGCCTCCCTGTGCTCAGCACAGACAAGTTCAAGACAGACTTTTACCATCAATGCAATGATGTGGA
GCTCATGGCCTACCTTGGCACCGTCACCAAAACCTGCAACACCATGAGCCAGCTTGTGAACAAGTTCAACATCCTTGATG
ACTGACAAGGCATCGGCAGGCGGATGCGGGGGCTCTTCTTT

Alignment

ORF - retro_cfam_1389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 82.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LVILNISDHWIRMRSQEGRPMQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQV
          L.ILNISDHWI.M.SQEG.PMQVIGALIGKQEGRNIEVMNSFELLSHTVE.KIIIDKEYYYT.EEQFKQV
Retrocopy LFILNISDHWICMCSQEGWPMQVIGALIGKQEGRNIEVMNSFELLSHTVEQKIIIDKEYYYTREEQFKQV

Parental  FKELEFLGWYTTGGPPDPSDIHVHKQV-CEIIESPLF-LKLNPMTKHTDLPVSVFESVIDIINGE-ATML
          FKELE..GWYTTG.PPDP.DI.VHKQV..EI.ES.LF.LKLNPMTK.TDLP.SVFESVIDIINGE.ATML
Retrocopy FKELECWGWYTTGRPPDPLDIQVHKQV<VEITESLLF<LKLNPMTKDTDLPISVFESVIDIINGE<ATML

Parental  FAELTYTLATEEAERIGVDHVARMTATGSGENST-VAEHLIAQHSAIKMLHSRVKLILEYVKASEAGEVP
          FAELTYTLATEEAE.IGV...A.MTATGSGENST..AEHLI.QH..IKML.SRVKLILEYVKASEA.EVP
Retrocopy FAELTYTLATEEAEGIGVKPMA*MTATGSGENST<MAEHLIVQHRTIKMLCSRVKLILEYVKASEA*EVP

Parental  FNHEI-LREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCNTMNQFVNKFNVLYDRQGIGR
          FNHEI.LRE.YALCHCLPVLSTDKFKTDFY.QCNDV.LMAYLGT.TKTCNTM.Q.VNKFN.L.D.QGIGR
Retrocopy FNHEI<LREPYALCHCLPVLSTDKFKTDFYHQCNDVELMAYLGTVTKTCNTMSQLVNKFNILDD*QGIGR

Parental  RMRGLFF
          RMRGLFF
Retrocopy RMRGLFF

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1389 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Canis familiaris	ENSCAFG00000014814	1 retrocopy	retro_cfam_1389 ,
Felis catus	ENSFCAG00000003561	1 retrocopy	retro_fcat_522,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Monodelphis domestica	ENSMODG00000004170	1 retrocopy	retro_mdom_220,
Otolemur garnettii	ENSOGAG00000016843	1 retrocopy	retro_ogar_1236,
Pteropus vampyrus	ENSPVAG00000005186	1 retrocopy	retro_pvam_690,