RetrogeneDB ID: retro_cfam_1385

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:71250500..71251905(-)
• Located in intron of: ENSCAFG00000015859

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP2
• Ensembl ID: ENSCAFG00000009977
• Aliases: None
• Description: CAP, adenylate cyclase-associated protein, 2 (yeast) [Source:HGNC Symbol;Acc:20039]

Sequence

>retro_cfam_1385
ATGGCTCACATGCAAAACCTGGCGGGAGGATTGGAGAAGGTGGTGGGCTGCCTGGAGGCCGTGTCCAATGCCTCTGACAT
GCACTGTGGGTATGGAGACAGCGCCCCAAAAGCAGGAACAGCTCCATATGTGCAAGCGTTTGACTCACTCCTTGCTGGTT
CTGGGGCAGAGTACCTGAAGCTCAGTAAAGAGACTGGGGGAGATGGGCAGGAATGTGTGGAGATGGCCCACACAGGTCTG
AAGTTGGAGCAAGCTCTCTCGGTTACAGCCTCTCAGTGTCAGCAGCCGGCAGGCAATAAGCTTTCTGACTTGTTGGCACC
CATCTCAGAGCAGATCCAAGAAGTGATAGGCTTCCAGGAGAAGAACCGAGGCAGCAAGTTGTTCAATCACCTGTCAGCTG
TCAGCCAAAGTATCCAGGCCCTGGGTTGGGTAGCTATGGCTCCCAAGCCTGGTCCCTATGTGAAAGAAATGAATGATGCT
GCCATGTTTCACACAAACCGAGTCCTCAAGGAGTACAAAGATGTCAATAAGAAGCATGTGGATTGGGTCAAAGCTCACTT
GAGTATATGGACAGAGCTACAGGCTTACGCTAAGGAGTTCCATACCACCGGACTGGCCTGGAGCAAAACGGGGCCTTGGC
ACAAGAACTGAGTGGATTGCCATCTGGACCCTCTGCTGGACCAGGTCCTTCTCCTCCCTCACCAGGCCCACCTCCCCCAC
AAGTCCCCCCCAGTTCAGGCTCAGATGAGTCTGCTTCCTGGTCAGCACTGTTTGCTCAGATGAATCAGGGGGAGAGCATC
ACACATGCCCTGAAACATGTATCTGATGACATGAAGACTCACAAGAACCCCGCCGTGAAGGCCCAGAGTGGTCCAGTATG
AAGTGGCCCCAAACCAGGGTCAGCCCATCCCCCAAGCCAACCACAAAGAAGGAGCCAGCTGTACTTGAACTGGAGGGGAA
GCAGTGGAGGGTGGAAAATGAGGAAAATGTTTCCAACCTGGTGATTGATGACACAGAGCTGAAACAGGTGGCTTACATAT
ACTAATGTGTCAACACAACATTGCGAATCGAGGGCAAAATAAACTCCATTACAGTAGGTAACTGTAAGAAACTCGGTCTG
GTGTTTGATGACGTGGTGGGCATTGTGGAGACCATCAATAGTAGGGATGTCAAAGTTCAGGTAATGGGTAAAGTGCCAAC
CATTTCCATCAACAAAACAGATGGCTGCCGTGTTTACCTGAGCGAGAATTCCCTGGATTGCGAGATAGTCAGTGCCAAAT
CTTCTGAGATGAATGTCCTCATTCCTACCGAAGGCGGTGGCTATAATGAATCCCCAGTCCCTGAGCAGTTCAAGACCCTA
TGGAATGGGGAGGAGTTGGTCTCCACAGTGACAGAAATTGCTGGA

Alignment

ORF - retro_cfam_1385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEMQGLMERLERVVGRLEVLSAESHRPPGDFGEINGVNGGVAPSVEAFDKLMNSMVAEFLKKSRILAGD
          MA.MQ.L...LE.VVG.LE..S..S....G..G.......G.AP.V.AFD.L.....AE.LK.S....GD
Retrocopy MAHMQNLAGGLEKVVGCLEAVSNASDMHCG-YGD-SAPKAGTAPYVQAFDSLLAGSGAEYLKLSKETGGD

Parental  VETHAEMVHSAFQAQRAFLLMASQHQQPQENDVAALLKPISEKIQEIQTFRERNRGSKMFNHLSAVSESI
          .....EM.H.......A....ASQ.QQP..N....LL.PISE.IQE...F.E.NRGSK.FNHLSAVS.SI
Retrocopy GQECVEMAHTGLKLEQALSVTASQCQQPAGNKLSDLLAPISEQIQEVIGFQEKNRGSKLFNHLSAVSQSI

Parental  PALGWIAVSPKPGPYVKEMNDAATFYTNRVLKDYKHSDLRHVDWVKSYLNIWSELQAYIKEHHTTGLTWS
          .ALGW.A..PKPGPYVKEMNDAA.F.TNRVLK.YK.....HVDWVK..L.IW.ELQAY.KE.HTTGL.WS
Retrocopy QALGWVAMAPKPGPYVKEMNDAAMFHTNRVLKEYKDVNKKHVDWVKAHLSIWTELQAYAKEFHTTGLAWS

Parental  KTGP-VASTASAL-SVLSPGPGLPPPPPPPPPPGPPPFFENEGRREESSPSRSALFAQLNQGEEITKGLR
          KTGP..A...S.L.S..S.GPG..PP.P.PPPP..PP.....G..E..S.S..ALFAQ.NQGE.IT..L.
Retrocopy KTGP<LAQELSGLPSGPSAGPGPSPPSPGPPPPQVPP---SSGSDESASWS--ALFAQMNQGESITHALK

Parental  HVTDDQKTHKNPSLRAPGGQTPSPTKSHTPGSRAPQSHP-PQKHAPVLELEGKKWRVEYQEGRNDLVIAE
          HV.DD.KTHKNP...A..G...S..K...PGS..P.S.P...K...VLELEGK.WRVE..E....LVI..
Retrocopy HVSDDMKTHKNPAVKAQSGPV*SGPK---PGSAHPPSQP<TKKEPAVLELEGKQWRVENEENVSNLVIDD

Parental  TELKQVAYIFKCNKSTLQMKGKINSITIDNCKKFGLVFDNVVGIVEVINSKDIQMQVMGKVPTISINKTE
          TELKQVAYI..C...TL...GKINSIT..NCKK.GLVFD.VVGIVE.INS.D...QVMGKVPTISINKT.
Retrocopy TELKQVAYIY*CVNTTLRIEGKINSITVGNCKKLGLVFDDVVGIVETINSRDVKVQVMGKVPTISINKTD

Parental  GCHIYLSEDALDCEIVSAKSSEMNVLIP-QDGDYREFPVPEQFKTVWDGSKLVTEPAEIMG
          GC..YLSE..LDCEIVSAKSSEMNVLIP...G.Y.E.PVPEQFKT.W.G..LV....EI.G
Retrocopy GCRVYLSENSLDCEIVSAKSSEMNVLIPTEGGGYNESPVPEQFKTLWNGEELVSTVTEIAG

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	0.04 RPM	46.32 RPM
SRP017611_brain	0.32 RPM	195.38 RPM
SRP017611_kidney	0.07 RPM	11.95 RPM
SRP017611_liver	0.00 RPM	10.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1385 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Canis familiaris	ENSCAFG00000009977	1 retrocopy	retro_cfam_1385 ,
Cavia porcellus	ENSCPOG00000008839	1 retrocopy	retro_cpor_1367,
Homo sapiens	ENSG00000112186	1 retrocopy	retro_hsap_1451,
Macaca mulatta	ENSMMUG00000001990	1 retrocopy	retro_mmul_2271,
Pan troglodytes	ENSPTRG00000017750	1 retrocopy	retro_ptro_987,