RetrogeneDB ID: retro_rnor_1180

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:18091513..18092290(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cap1
• Ensembl ID: ENSRNOG00000013492
• Aliases: Cap1, Mch1
• Description: Adenylyl cyclase-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q08163]

Sequence

>retro_rnor_1180
GTGCAAAATCTTGTAGACAGATTGAAGAGGGCGGTGGGCTGCCTGCAGGCAGTGTCACACACCTCTGACATGCACTGTGG
ATGAGGAGACAGTCCTTCAAAAGGAGTAATTCCATATGTGCAAGCATTTGACTCTCTGCTTGCCATTCCCATGGAGGAGT
ACTTGACGATGAGTAAGGAGATTTGGGGAGACACACAGAAACACGCGGAGATGGTCCGCACAGGCCTGAAGTTGGAGCGA
GCTCTCCTGGTTACAGCTTCATGGTGCAAGCAGTCAGCTAGTAATCAACTTTCTGACCTGTTGGCTCCTGTCTCAGAGCA
GATCCAAGACGTTCTCCTTCCTGGAGAAGGACCAAGGCAGCAAGATTTTCGATTCTGTGTCAGCTATCCGTGAAAGCATC
CAGGCCCTGGGATGAGTCGCTCTGACTGAGAAACCTGGCCTCTTTGTGAAATAGATAAATGATGTGGTCATGTTTTACAA
AAACCAAGTCCACAAAGAAGTACAGAGACATGGAATAGAAGCATGTGGGCTGGGTCAGAGACTTTCTTGAGCTTATGGAT
AGAACAACAGGCTCACATTAAGAAGTTCCATGCCACTGGCCTGGCCTGGAGCAAGATGGCACCTGTGGCAAAAGAACTGA
GTGGATGGCCCTATGGACCTTTTGTGGGATCGGGCCCACCTCCTCCCACACCGGGCTCACTTCCTCCCCTAATCCCTATC
AGTTCTGGCTCTGAGAACTCAGCTTCACACTCAGCACTGTTTGCACAGATTAAGGAG

Alignment

ORF - retro_rnor_1180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.58 %
• Parental protein coverage: 54.64 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MQNLVERLERAVGRLEAVSHTSDMHCGYGDSPSKGAVPYVQAFDSLLANPVAEYLKMSKEIGGDVQKHAE
          .QNLV.RL.RAVG.L.AVSHTSDMHCG.GDSPSKG..PYVQAFDSLLA.P..EYL.MSKEI.GD.QKHAE
Retrocopy VQNLVDRLKRAVGCLQAVSHTSDMHCG*GDSPSKGVIPYVQAFDSLLAIPMEEYLTMSKEIWGDTQKHAE

Parental  MVHTGLKLERALLVTASQCQQPAGNKLSDLLAPISEQIQEVITFRE-KNRGSKF-FNHLSAVSESIQALG
          MV.TGLKLERALLVTAS.C.Q.A.N.LSDLLAP.SEQIQ.V....E.......F.F...SA..ESIQALG
Retrocopy MVRTGLKLERALLVTASWCKQSASNQLSDLLAPVSEQIQDVLLPGE<RTKAARF<FDSVSAIRESIQALG

Parental  WVALAAKPGPFVKEMNDAAMFYTNRVLKE-YRDVDKKHVDWVR-AYLSIWTELQAYIKEFHTTGLAWSKT
          .VAL..KPG.FVK..ND..MFY.N.V.KE.YRD...KHV.WVR...LS.W.E.QA.IK.FH.TGLAWSK.
Retrocopy *VALTEKPGLFVK*INDVVMFYKNQVHKE>YRDME*KHVGWVR>TFLSLWIEQQAHIKKFHATGLAWSKM

Parental  GPVAKELSGLPSGPSVGSGPPPPPPGPPPPPVPTSSGSDDSASRSALFAQINQ
          .PVAKELSG.P.GP.VGSGPPPP.PG..PP..P.SSGS..SAS.SALFAQI..
Retrocopy APVAKELSGWPYGPFVGSGPPPPTPGSLPPLIPISSGSENSASHSALFAQIKE

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
SRP017611_brain	0.00 RPM	230.00 RPM
SRP017611_kidney	0.00 RPM	134.54 RPM
SRP017611_liver	0.00 RPM	43.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1180 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1180 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1265

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Homo sapiens	ENSG00000131236	2 retrocopies	retro_hsap_2666, retro_hsap_664,
Gorilla gorilla	ENSGGOG00000027527	2 retrocopies	retro_ggor_1860, retro_ggor_575,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Mus musculus	ENSMUSG00000028656	1 retrocopy	retro_mmus_1265,
Nomascus leucogenys	ENSNLEG00000012077	2 retrocopies	retro_nleu_1600, retro_nleu_2221,
Otolemur garnettii	ENSOGAG00000005492	1 retrocopy	retro_ogar_299,
Pongo abelii	ENSPPYG00000001496	4 retrocopies	retro_pabe_2212, retro_pabe_2358, retro_pabe_2415, retro_pabe_584,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180 ,