RetrogeneDB ID: retro_cfam_1083

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:49570066..49571084(-)
• Located in intron of: ENSCAFG00000005809

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNB1
• Ensembl ID: ENSCAFG00000019216
• Aliases: None
• Description: Canis lupus familiaris guanine nucleotide binding protein (G protein), beta polypeptide 1 (GNB1), mRNA. [Source:RefSeq mRNA;Acc:NM_001003236]

Sequence

>retro_cfam_1083
ATGAGTGAACTTGACTAGTTATGGCAGGAGGCCGAGCAGCTTAAAAACCAAATTAGGGATGTTAGAAAGGCATGTGCAGA
TGTAACTGTCTCTCAGATCACAAACAACATCGACCCAGTAGGAAGAATCCAGATGCACACACCAGGAGAACGCTGAGGGC
ATTTGGCCAAAACTTATGCCATGCATTGGGGCACAGATTCCAGGCTTCTGGTCAGTGCCTCACAGGATAACAAACTGATC
ATCTGGGATAGCTACGCTACAAACTAGGTCCATGCCAACCCTCTGCGTTCCTCATGGGTCATGACCTGTGCATATGCCCC
TTCTGGGAACTATGTGGCCTGTGGTGGCCTGGATAACATTTGCTCCATTTACAATCTGAAAACTCGTGAAGGGAATGTAC
GTGTGAGCCGTGAACTGGCAGACATACAGGTTATCTGTCCTGCTGCCGCTTCCTGGATGACAATCAGATCATCACCAGCT
CTAGGGACACCACTTGTGCTCTGTGGGACATTGAGACCAGCCAGCAGTCAACCACATTCACTGGACACGCTGGGGATGTT
ATGAGCCCTTCTCTCGCTCCCAACACCAGACTGTTTGTCTCTGGTGCTTGTGATGCATCAGCCAAATTCTGGGATGTGCA
AGAAGGGATGTGCCGGCAAACTTTCACCGGCCACGAGTCCGACATCAATGCCATCTGTTTCTTTCCAAACGGCAATGCAT
TTGCACTGGCTTGGATGATGCCACCTGTAGGCTGTTCAACCTTCGTGCACAGCAGGAGGTCATGACTTATTCCCATGACA
ACATCATCTGTGGGATCACCTCGGTGTCTTTCTCCAAGAGCGGGTGCCTCCTCCTCACAGGGTACGATGACTTCAACTGC
AATGTGTGGGACGCACTCAAGGCCGACAGAGCAGGTGTCTTGGCTGGGAATGACAACCGTGTCAGCTGCCTGGGGGTGAC
TGACGATGGGATGGCTACGGCGACACGGTCCTGGGATAGCTTCCTCAAGATCTGGAAC

Alignment

ORF - retro_cfam_1083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLL
          MSELD.L.QEAEQLKNQIRD.RKACAD.T.SQITNNIDPVGRIQM.T.....GHLAK.YAMHWGTDSRLL
Retrocopy MSELD*LWQEAEQLKNQIRDVRKACADVTVSQITNNIDPVGRIQMHTPGER*GHLAKTYAMHWGTDSRLL

Parental  VSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELA
          VSASQD.KLIIWDSY.TN.VHA.PLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELA
Retrocopy VSASQDNKLIIWDSYATN*VHANPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELA

Parental  G-HTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAK
          ..HTGYLSCCRFLDDNQI.TSS.DTTCALWDIET.QQ.TTFTGH.GDVMS.SLAP.TRLFVSGACDASAK
Retrocopy D<HTGYLSCCRFLDDNQIITSSRDTTCALWDIETSQQSTTFTGHAGDVMSPSLAPNTRLFVSGACDASAK

Parental  LWDVREGMCRQTFTGHESDINAICFFPNGNAFA-TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSF
          .WDV.EGMCRQTFTGHESDINAICFFPNGNAFA.TG.DDATCRLF.LRA.QE.MTYSHDNIICGITSVSF
Retrocopy FWDVQEGMCRQTFTGHESDINAICFFPNGNAFA<TGLDDATCRLFNLRAQQEVMTYSHDNIICGITSVSF

Parental  SKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
          SKSG.LLL.GYDDFNCNVWDALKADRAGVLAG.DNRVSCLGVTDDGMA.AT.SWDSFLKIWN
Retrocopy SKSGCLLLTGYDDFNCNVWDALKADRAGVLAGNDNRVSCLGVTDDGMATATRSWDSFLKIWN

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	420.79 RPM
SRP017611_brain	0.48 RPM	302.48 RPM
SRP017611_kidney	0.40 RPM	193.95 RPM
SRP017611_liver	0.44 RPM	64.10 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1083 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1083 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019216	1 retrocopy	retro_cfam_1083 ,
Echinops telfairi	ENSETEG00000020012	1 retrocopy	retro_etel_1984,
Rattus norvegicus	ENSRNOG00000016638	1 retrocopy	retro_rnor_1660,