RetrogeneDB ID: retro_cpor_735

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:1740298..1741701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC1
• Ensembl ID: ENSCPOG00000013839
• Aliases: None
• Description: None

Sequence

>retro_cpor_735
CTACTTACATGTGAATGTTATGAATTATTTGTGAACATTTTGGTTGTGTGTGGCTTTATCATAGTTTCAGATAGATCCAG
TGGGATTCATAAAATCCAAGATGATCTGCATCCTTCAGAAACCCTTCACTTAACCAGTTCACATTCCTTCAAGTCCACTG
AGTGTCTTCTTCTCAGTCTGCTCCATGGAGACAAAAGCAAAGAAGAATCAGATTCTCCAGAGAGACTCCAGGTAAGTGAT
CAAGAATTTCAAGAAGAATGCGCTAAGAAAATACAGCTAGTTAACTTAAGAAGCAGAAGAGTCAGAGCTAATGACATAAT
GGGAGAAAGTTGTCACAGTCTGATAAGCTTGAGTAGCTTGCATGTTCTGTCCTCTAACATCAAACCGAGGTGCTCTGCTT
TGGAGGGAATTGTAGACACACCAGGCTATTCCTGTAAAAAGATGTGAAGTGCCTTCCATTGGTTTGTTCTGAATACAGAA
AAACACAAGACTGAACAATGTTTAGAATCAAAGCCCTAACCGGAGTCCCTGTTGGATCTGCATTCAGAGGGAAGTGCTCA
CAAGCCACTCTGCAGTGGTGGCTTCAAGAGAACTTCTGCTTTGACTGTCAAAGACCAAGAAGAGTCTTGTCCTGGGGAGT
GAAGGCCCAAACAGCTTTGCAGGTCCCAAAGTCTACTTTAAAGAATCAGTTCAAGACAGAATAGCTATGTCAATACACCA
GTGGTGGAAGTTGTCATGAAACCAAACCCTGCACACAGCAGCACAAGTGTGCAAAGACTATGGAAAGTAAACTCAGGGAG
GACTGCATCACAATCAATAAAAGACTGTGCAAAAGTACCATAGAACTCCCAGAAAACTCTTTACCTCCAGCTTCTATACT
GACTGGCAAACAAAGCTTGCTTCAGCCCCACCTGGAGAGAGTTGCAGTCAGCACACTACAGTTATGCTGTTTGCTGCTTT
CCCCACCAAACCGTAGAAAGATACAGCTTCTAATGTGCATGATTTCTTGAATGAGTGAAAATGTCCACATGCCCAAACTC
CAGGACGCCATGGGTACAAGGGTGCTGATGATACACACTTTTTCTCGGTGTGTGCTGTGCTGTGCAGAAGAAGTGAACAT
GGATGAGTTGCTTGCTGCAAGATTAGTTTCTTTCCTAATGGATCATCAGCAGGAAATTCTTCAGGTGCCCTCTTACTTAC
AGGCCTCAGTGGACAAACAACTAGACTACTTACAAAAGGGCAACACTAAAAGTCCTGGGGATGGGCTCATTGTTCCTCTG
CTGACTTTCTTTTACTGTAAACAGATCAGTGCTCAGGAGTTTGATAAGCAGAAGGTTTCTACCTCTGAAGCTACCATTGC
AGAACTTCTGGAGAATATTGTTAAAAGCAAGAGTTTACCTCTG

Alignment

ORF - retro_cpor_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 84.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLTYEYYELFVNILVVCGCITVSDRPSGTHKIQDDPQPSETLHLTSSHSFKSTECLLLSLLHRDKSKEDS
          LLT.E.YELFVNILVVCG.I.VSDR.SG.HKIQDD..PSETLHLTSSHSFKSTECLLLSLLH.DKSKE.S
Retrocopy LLTCECYELFVNILVVCGFIIVSDRSSGIHKIQDDLHPSETLHLTSSHSFKSTECLLLSLLHGDKSKEES

Parental  DFPERLQLSDHGFQEGHAKKMQLVNLRSRRVRTRDGMGGSCHSLTGLSSSRALSASIKPRCSSLEGIVDT
          D.PERLQ.SD..FQE..AKK.QLVNLRSRRVR..D.MG.SCHSL..LSS...LS..IKPRCS.LEGIVDT
Retrocopy DSPERLQVSDQEFQEECAKKIQLVNLRSRRVRANDIMGESCHSLISLSSLHVLSSNIKPRCSALEGIVDT

Parental  PGYSCARVSSAFQHSVLSAVRHKSEQCLESEPKQESLLDLHSGGRTHKPLCSGGFRRISALTVRDQEESG
          PGYSC....SAF...VL....HK.EQCLES.P..ESLLDLHS.G..HKPLCSGGF.R.SALTV.DQEES.
Retrocopy PGYSCKKM*SAFHWFVLNTEKHKTEQCLESKP*PESLLDLHSEGSAHKPLCSGGFKRTSALTVKDQEESC

Parental  SGDCRPQPLCRSQSLLLRSSSRRNSYVNTPVAEVVMKPTLGHGSTRVHR-AMESELREDCVTINKRLCKS
          .G..RP..LCRSQSLL.R.SSR.NSYVNTPV.EVVMKP...H.ST.V.R..MES.LREDC.TINKRLCKS
Retrocopy PGE*RPKQLCRSQSLL*RISSRQNSYVNTPVVEVVMKPNPAHSSTSVQR<TMESKLREDCITINKRLCKS

Parental  TVELSENSLPPASAVLTGTQSLLQPHLERVAVSALQLCCLLLPPPNRRKLQLLMRMMARMSGNVDLPRLH
          T.EL.ENSLPPAS..LTG.QSLLQPHLERVAVS.LQLCCLLL.PPNRRK.QLLM.M...MS.NV..P.L.
Retrocopy TIELPENSLPPAS-ILTGKQSLLQPHLERVAVSTLQLCCLLLSPPNRRKIQLLMCMIS*MSENVHMPKLQ

Parental  DAMGTRALMIHTFSRCVLCCAEEVDLDELLAARLVSFLMDHQQEILQVPSYLQAAVDKQLDCLQKGQITG
          DAMGTR.LMIHTFSRCVLCCAEEV..DELLAARLVSFLMDHQQEILQVPSYLQA.VDKQLD.LQKG....
Retrocopy DAMGTRVLMIHTFSRCVLCCAEEVNMDELLAARLVSFLMDHQQEILQVPSYLQASVDKQLDYLQKGNTKS

Parental  PGDGLLAPLPTFSYCKQISTQEFDEQKVSTSQAAIAELLESLMKNKSLPL
          PGDGL..PL.TF.YCKQIS.QEFD.QKVSTS.A.IAELLE...K.KSLPL
Retrocopy PGDGLIVPLLTFFYCKQISAQEFDKQKVSTSEATIAELLENIVKSKSLPL

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	0.52 RPM
SRP017611_kidney	0.00 RPM	1.05 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP040447_lung	0.00 RPM	2.47 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.29 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_735 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_735 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013839	1 retrocopy	retro_cpor_735 ,
Homo sapiens	ENSG00000024526	2 retrocopies	retro_hsap_1545, retro_hsap_4206,
Gorilla gorilla	ENSGGOG00000016316	1 retrocopy	retro_ggor_1176,
Macaca mulatta	ENSMMUG00000017766	1 retrocopy	retro_mmul_1176,
Mus musculus	ENSMUSG00000028175	1 retrocopy	retro_mmus_3028,
Nomascus leucogenys	ENSNLEG00000009334	1 retrocopy	retro_nleu_2931,
Otolemur garnettii	ENSOGAG00000000934	1 retrocopy	retro_ogar_1907,
Pongo abelii	ENSPPYG00000001248	1 retrocopy	retro_pabe_3441,
Pan troglodytes	ENSPTRG00000000847	2 retrocopies	retro_ptro_1041, retro_ptro_2855,