RetrogeneDB ID: retro_cpor_1470

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:26828447..26829444(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZSCAN4
• Ensembl ID: ENSCPOG00000005419
• Aliases: None
• Description: None

Sequence

>retro_cpor_1470
ATGGCCTTAGATCTCGGAAATTCATTTTTCCATGAGCCATTCCCAAACAAACTTGAATCAGAAAACTTAGAGTTTAAATC
AACTCAAGGATCTGCTGTCCCAAGGAGAGTGATCTCTGAATTCTCAAGCACTGAGCTCAACACATTTCAGTACACTGATA
AGTCATGGGCGAGGAGGAAGTACAAAGTCTACAAATTTTTTCCCTCATGACTGCAACGAGAAAAGCATAGCAAGGATGCG
ATTACGTCTCAGTTAACCATGGAGCAGTTTATGCTTAGTGACCTCGCCAGGGACAAGACTATGTTGAAAAAGAAACAGAA
ATCGAGTTATAAAAACCTAGAGAAATTTGTGGAAGACCTGACAGATGGTTGTATGAAGCCACCTGTATTAGTCTATGTCT
GCTTGCAAGGACAGGAAGCTCTCTTTTCTGAGGATACGTCCTGAAAAGAAGTCATTGTTAATTTTTAAAAACAGCTGTCA
GCAGAAACCTTAAGAGGAGAGAATATGTGAACATCTTGCCAGGTTTCCCAAAATGCTCCTTTGGAAACAAGACAAGGAAG
TGAATATAAAGTAGATGGCTGCAGCAATTTCTGAGAAATTACTCAAGTAAATGGCAATATTACTAATCCAGGAAAAGAGA
TAGCTCTCCTTCTCATCATCCTGGAAGAGAACTGTCCTAGGCCTGAAAAGAAGGGTGTTTCTTGGGAGAGCCCACCCAAC
TGCAGAAGAGCAAGGCTAGACACCTAAAGATTGCAGGAAGAGTCCCAGAAGGGACCTTCTAACCAAGATGTCCTATGGAT
GTGGGACCAGGATTGTTCTCTAGGTCACACAGTCCTCCCCTGAGCTGACCCTACCTATCACACCAATGAATGAAACTGCA
CCTGTGAGGGACCCCAAAAAAAGATTCCATGGATACCCAGGATCATACAAATGGCCCAAGACTTTTAGGTAGCTCACCCA
TTTATTCACCCACAAAAGAAGACACAGGAATGAGAGG

Alignment

ORF - retro_cpor_1470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALDLRKSFCQELSSNNLESEDLEFSSTQGFAVPKREISAFSSIQLNSLQYSDNSEARKELQRLYEFFHS
          MALDL..SF..E...N.LESE.LEF.STQG.AVP.R.IS.FSS..LN..QY.D.S.AR......Y.FF.S
Retrocopy MALDLGNSFFHEPFPNKLESENLEFKSTQGSAVPRRVISEFSSTELNTFQYTDKSWARRKY-KVYKFFPS

Parental  WLQPENHSKDQIIAQLAMEQFMLSGRCRDKSILKKKWESSGKNLEKLLEDLTDDCMKPPVLVHVCMQGQE
          .LQ.E.HSKD.I..QL.MEQFMLS...RDK..LKKK..SS.KNLEK..EDLTD.CMKPPVLV.VC.QGQE
Retrocopy *LQREKHSKDAITSQLTMEQFMLSDLARDKTMLKKKQKSSYKNLEKFVEDLTDGCMKPPVLVYVCLQGQE

Parental  ALFSEDMPLKEVIAHLTKQSSAKTFTA-GMGTAHQVSQNAPLGTRQGNEHEEDGCTSSWEVTQVNDYITN
          ALFSED...KEVI....KQ.SA.T.....M.T..QVSQNAPL.TRQG.E...DGC....E.TQVN..ITN
Retrocopy ALFSEDTS*KEVIVNF*KQLSAETLRGENM*TSCQVSQNAPLETRQGSEYKVDGCSNF*EITQVNGNITN

Parental  PGKEIVSLLIIPEANDPTPVEESASWENTHSSRKARPVICGLQEESQKGPSYQDV-PMDVGPGSSSLPH-
          PGKEI..LLII.E.N.P.P.....SWE.....R.AR.....LQEESQKGPS.QDV.PMDVGPG..S..H.
Retrocopy PGKEIALLLIILEENCPRPEKKGVSWESPPNCRRARLDT*RLQEESQKGPSNQDV<PMDVGPGLFSRSH<

Parental  QSSSEPV-SNHHCSEGNSACE-ESQERFHESPKSYKCEECPKTFKYLSHFLAHQRCHRSFR
          QSS.E......H..E.N..CE.....RFH..P.SYK....PKTF..L.H...H.R.HR..R
Retrocopy QSSPELT<PTYHTNE*NCTCE>DPKKRFHGYPGSYK---WPKTFR*LTHLFTHKRRHRNER

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	0.12 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.03 RPM	0.10 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1470 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1470 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470 , retro_cpor_285,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408,