RetrogeneDB ID: retro_cpor_1367

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_72:7727059..7728480(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP2
• Ensembl ID: ENSCPOG00000008839
• Aliases: None
• Description: Adenylyl cyclase-associated protein [Source:UniProtKB/TrEMBL;Acc:H0VD91]

Sequence

>retro_cpor_1367
ATGGCCGACATGCAAAATCTGGTGGAAAGGTTGGAGAGGGCAGTGGGCCGCCTGGAGGCAGCATCCCGGCCCTCTGACAC
GTGCCGGGGGAATGGGTATGGAGTCGATCCTTCACAGGGAGCAGCTCCATATGTGGAAGCGTTTGACTCACTGCTTGCAG
GTCCTGTGGCAGAGTACTTGAAGATCAGTAAAGAGCTCGGGGGAGATGTACAGAAACATGCAGAGATGGTCCACACAGGT
CTGAAGTTGGAGCGAGCTCTCCTGGCTATCGCTTCTCAGTGCTAGCAGCCAGCCGGTAATAAGCTTTCTGATTTATTGGC
ACCCATCTCAGAGCAGATCCAAGAAGTGATAAACTTTCGGGAGAAAAACCGGGACAGCAAGTTGTTCAATCACCTGTCAG
CTGTCAGTGAAAGCATCCAGGCCTTGGGTTGGGTGGCAATGGCTCCTGCACCTGCCCCTATGTGAAAGAAATGAATGATG
CGGCCATGTTTTATACAAACAGAGTCCTCAAGGAGTACAAAGATGTGGATAAGAAGCACGTGGACTGGGTGAAAGCTTAC
CTGAGTATATGGACAGAACTGCAGGTTTATATTAAGGAGTTCCACACCACTGGCCTGGCCTGGAGCAAAACGGGGCCTGG
GGCAAGAGAACTGAGTGGACTGCCATCTGGACCCTCTGCTGTATCCGGTCCTCCTCCCCCTCTCCCGGGTCCTCCTTCTC
CTCCAGTCGCCACCAGTTCAGGCTCTGATGACTCTGCTTCCCGTTCAGCACTGTTTGCGCAGATTAATCAGGGAGAGAGC
ATTACACATGCCCTGAAGCATGTATATGATGATATGAAGACTCACAAGAACCCCGCCCTGAAGGCTCAGAGTGGTCCAGT
ACGCAGTGGCCCCAAACCATTCTCTGCACCTAAACCCCAAACCAGTTCATCCCCCAGACCAGCCACAAAGAAGGAGCCTG
CTCTACTTGAACTGGAGGGCAAGAAGTGGAGAGTGGAAAACCAGGAGAATATTTCCAACCTGGTGATTGAGAACACAGAG
TTGAAACAGGTGGCTTACATATTCAAGTGTGTCAACACAACATTGCAAATCAAGGGCAAAATTAACTCCATTATAGTAGA
TAACTGTAAGAAACTTGGTCTGGTATTCGATGATGTGGTGGGCATTGTGGAGATAATCAATAGCAGAGATGTCAAAGTTC
AGGTAATGGGTAAAGTGCCAACCATTTCCATTAATAAAACAGATGGCTGCCACGTTTACCTGAGCAAGAATTCCCTGGAT
TGTGAGATAGTCAGTGCCAAATCTTCTGAGATGAACGTCCTCATACCTACAGAAGGTGGCGATTTTAATGAGTTTCCAGT
TCCTGAGCAGTTTAAGACCCTATGGAATGGGCAGAAGTTGGTCATTACAGTGACAGAAATT

Alignment

ORF - retro_cpor_1367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADLQGLVERLEHAVSRLEQLSAESQQPPGGFGEVNGVNGGVAPSVEAFDKLMNGMVAEFLRNSRILAGD
          MAD.Q.LVERLE.AV.RLE..S..S....G....V.....G.AP.VEAFD.L..G.VAE.L..S..L.GD
Retrocopy MADMQNLVERLERAVGRLEAASRPSDTCRGNGYGVDP-SQGAAPYVEAFDSLLAGPVAEYLKISKELGGD

Parental  VETHAEMVHGAFQAQRAFLVMASRYQQPQENEVAALLKPISEKIQEIQTFRERNRGSNMFNHLSAVSESI
          V..HAEMVH......RA.L..AS...QP..N....LL.PISE.IQE...FRE.NR.S..FNHLSAVSESI
Retrocopy VQKHAEMVHTGLKLERALLAIASQC*QPAGNKLSDLLAPISEQIQEVINFREKNRDSKLFNHLSAVSESI

Parental  PALGWIAVSPKPGP-YVKEMNDAATFYTNRVLKDYKHSDLRHVDWVKSYLNIWSELQAYIKEHHTTGLTW
          .ALGW.A..P.P.P.YVKEMNDAA.FYTNRVLK.YK..D..HVDWVK.YL.IW.ELQ.YIKE.HTTGL.W
Retrocopy QALGWVAMAPAPAP<YVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQVYIKEFHTTGLAW

Parental  SKTGPVASPASAFSVLSAGPG-LPPPPPPPPPPGPPPLFENEGTKEASSPSRSALFAQLNQGEAITKGLR
          SKTGP.A...S....L..GP.....PPPP.P.P..PP.....G.....S.SRSALFAQ.NQGE.IT..L.
Retrocopy SKTGPGARELSG---LPSGPSAVSGPPPPLPGPPSPPVATSSGSDD--SASRSALFAQINQGESITHALK

Parental  HVTDDQKTYKNPSLRAQ-GQTRS-PTKSHTPSPTSPKAHSPQT--HAPVLALEGKKWRVEYQEDRNDLVI
          HV.DD.KT.KNP.L.AQ.G..RS.P.....P.P.......P.T......L.LEGKKWRVE.QE....LVI
Retrocopy HVYDDMKTHKNPALKAQSGPVRSGPKPFSAPKPQTSSSPRPATKKEPALLELEGKKWRVENQENISNLVI

Parental  SETELKQVAYIFKCDRSTLQIKGKINSITIDNCKKFGLVFDNVVGIVEVINSRDIQIQVMGRVPTISVNK
          ..TELKQVAYIFKC...TLQIKGKINSI..DNCKK.GLVFD.VVGIVE.INSRD...QVMG.VPTIS.NK
Retrocopy ENTELKQVAYIFKCVNTTLQIKGKINSIIVDNCKKLGLVFDDVVGIVEIINSRDVKVQVMGKVPTISINK

Parental  TEGCHIYLSEDALDCAVVSAKSSEMNVLIPQE-GDYREFPVPEQFKTTWDGSKLITEPAEI
          T.GCH.YLS...LDC..VSAKSSEMNVLIP.E.GD..EFPVPEQFKT.W.G.KL.....EI
Retrocopy TDGCHVYLSKNSLDCEIVSAKSSEMNVLIPTEGGDFNEFPVPEQFKTLWNGQKLVITVTEI

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	2.93 RPM	208.61 RPM
SRP017611_kidney	3.14 RPM	1.05 RPM
SRP017611_liver	2.00 RPM	0.17 RPM
SRP040447_lung	5.04 RPM	3.98 RPM
SRP040447_skeletal_muscle	1.06 RPM	202.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1367 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1367 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
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,