RetrogeneDB ID: retro_cpor_743

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:16992415..16993062(+)
• Located in intron of: ENSCPOG00000009894

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC34
• Ensembl ID: ENSCPOG00000023874
• Aliases: None
• Description: None

Sequence

>retro_cpor_743
GCTCCACCGCTGGTGCCCAGCTCCTAGAACATGCTGCTGCTGGAGCACAAGGGGCTGCAGTAAGCATCGGTAGAGGGCTT
CTGCATGGCTCTGATAGATGAAGACAGCCTATACAACTGGGAGGTGTTCATCTTTGGGCCACCTAATACCTACTAGAAGG
GCAGCTACTTCAAATCACAGCTCAAGTTCTCCATGAACTACCTGTACTCCCCACCAACTTTCCTTACCAAGATGTGGAAC
CCAAACATTTATGAGATAGGGAATATGTGCATCTGCATCCTGCACCCCCAAGTGGACAGCCCCAGAGTGGGGAGCTCCCC
TTGGAGCAGTGGAACCACTCTCAGAATATCAAGACCATCCTCTTGAGCATGATCTCCCTGCTGAACTAACCCAACACCTT
CTGGGTGGCCAATGTGGATGCCTAGGTGATGTACAGGAAGTGGAAGCAGAGCAAGGGCAAGAATGGCAAGTACATTACCT
AGAAGCAAGTCCTAGGAACTAAGGTGGATGCAGAGCATGACTTCATGAAGGTACCTACCACACTGGCCAAATACTATGTG
ACAAGCAAGGTGCCAGTGTCCAAGGAGGGCACGGACTACTTGGAAGATGGTGAAGCTGATGAAGAGGCTTGCAGCTGCCT
TGAGGAC

Alignment

ORF - retro_cpor_743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.25 %
• Parental protein coverage: 99.1 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARPLVPSSQKALLLELKGLQEEPVEGFRVALVDEGDLYNWEVAIFGPPDTYYEGGYFKARLKFPIDYPYS
          A.PLVPSS...LLLE.KGLQ...VEGF..AL.DE..LYNWEV.IFGPP.TY..G.YFK..LKF...Y.YS
Retrocopy APPLVPSS*NMLLLEHKGLQ*ASVEGFCMALIDEDSLYNWEVFIFGPPNTY*KGSYFKSQLKFSMNYLYS

Parental  PPAFRFLTKMWHPNIYETGDVCISILHPPVD-DPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPA
          PP...FLTKMW.PNIYE.G..CI.ILHP.VD..PQSGELP.E.WN..QN..TILLS.ISLLN.PNTF..A
Retrocopy PPT--FLTKMWNPNIYEIGNMCICILHPQVD<QPQSGELPLEQWNHSQNIKTILLSMISLLN*PNTFWVA

Parental  NVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVPTTLAEYCVKSKAPVPEEGPELFYEDD
          NVDA.VMYRKWK.SKGK...Y..I..KQVLGTKVDAE.D..KVPTTLA.Y.V.SK.PV..EG........
Retrocopy NVDA*VMYRKWKQSKGKNGKY--IT*KQVLGTKVDAEHDFMKVPTTLAKYYVTSKVPVSKEGTDYLEDGE

Parental  CEDGSCLGDED
          .....C...ED
Retrocopy ADEEACSCLED

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	18.41 RPM
SRP017611_kidney	0.00 RPM	18.84 RPM
SRP017611_liver	0.00 RPM	11.67 RPM
SRP040447_lung	0.00 RPM	22.27 RPM
SRP040447_skeletal_muscle	0.00 RPM	26.50 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_743 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_743 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023874	1 retrocopy	retro_cpor_743 ,
Macropus eugenii	ENSMEUG00000000812	1 retrocopy	retro_meug_1683,
Mus musculus	ENSMUSG00000020307	1 retrocopy	retro_mmus_23,
Ochotona princeps	ENSOPRG00000001017	1 retrocopy	retro_opri_464,
Pan troglodytes	ENSPTRG00000010153	1 retrocopy	retro_ptro_52,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,
Tursiops truncatus	ENSTTRG00000000391	2 retrocopies	retro_ttru_1142, retro_ttru_98,