RetrogeneDB ID: retro_cpor_70

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:10734096..10736112(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000004690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSRP1
• Ensembl ID: ENSCPOG00000000480
• Aliases: None
• Description: None

Sequence

>retro_cpor_70
ATGGCAGAGATGCTTGAGTTCAGTGACATCTATCAGGAGATGAAAGGCTCCATGAAGGAGGGTCATCTAAGGTTGGACCA
TCAGGGTATCATCTTCAGGCACAGCAAGACAGGTAAAGTGGACAACATCCAGGCCTGTGAGCTGATGGAAGGTGTCTGGC
GCAGGGTATCTCTGGGTCATGGACTTAAACTGCTCCTAAAGCATGGCCATGTCTACAGATACGATGGCTTCCAAGAATCG
GAGTTTCAGAGACTCTCTCATTTCTTCAAGACTCACTATCATCTTGAGCTCAAGGAGAAGGACCTCTGTGTAAAGGGCTG
GAACTGGGGGACAGTGAAGTTTGGTGAGCAGCTTCTCTCCTTTGACATTGGCAGCCAGTCAGTCTTCGAGATACCCCTCA
GCAACGTCTCCCAGTGTACCACAGCCAAGAATGAAGTGACTCTGGAGTTCCACCAGAGTGATGATGTAGAAGTCTCCCTT
GTGGAGATGCGCTTCTATGTTCCTCCTACCCAGGAGGAAGGTGTGGACCTGGTCCAGGCCTTTGCCCAGAATGTGCTGTC
CAAAGCAGACGTAATCCAGGCCACTGCAGATGCCATCTGCATCTTCCAGGAGCTGCAGTGCCTGACTCCCCGAGGTCGTT
ATGACATTCGCATCTATCCCACCTTCCTGCACCTACACGGCAAAACCTTTGACTACAAGATCTCCTTCTCCATGGTTCTG
CACCTCTTCCTGCTGCCCCACAAGGACCAACGCCAAATGTTCTTTGTGATCAGCCTGGATCCCCCTATCAAGCAGGGCCA
GACCCGTTACCACTTCCTCATCCTTCTGTTCTCCAAGGAGGAGAACATCACTTTGACTCTCAACATGAATGAGGAGGAAG
TAGAGAAGCGCTTTGAGGGGCAGCTAACCAAGACCATGGTAGGGTCACGTTATGAGGTGTTCAGCCGGGTCATGAAAGCC
CTTGTAAACCACAAGATCACAGTCCCTGGTAACTTCCAAGGGCACTTGGGGGCCAAGTGCATCGCCTGTTCCTACAAAGC
CAGCTCAGGGCTGCTGTATCCGCTGGAGCAGGACTTTATCTATGTCCACAAGCCACCTGTCCACGTCCACTTCCATGAGA
TCGCCTGTGTCAACTTTGCCCGTGGTATCACCACCACTCGCTTCTTTGATTTGGAGATTGAGACCAAGCAGGGCACTCAG
TTCACCTTCAGCAGCATCCAGAAGGAGGAGTACGGAAAGCTGTTTGATTTCATCAGTGCCAAAAAGCTTAACATCAAAAA
CCAAGAATTGAAAGATGGCAAAAATCCAAAATACCGCAAATACACTGACTCTGATGAAGAACTGCATGATGCCTACCTGG
AGAGGATGAAGGAAGAGGGGAAGATCCGGGAAGAGAATCCAAATGACAGCAGCGATGACTTGGGAGAGGAAATGGATGAG
TCCTTCAAGCCTGGAGAGGAAGAGGAGGAAGAGGTGGCGGAGGAGTTTGACAGCAATGCCTCTACCACCAGCTCCTTCAG
TAATGAGGGTGACAGTGACCAGGATGAGAAGGAGCAGAAACAGCTCCAAAGGGCCAAGACAGCCAAGGATCACAAGGACC
ACAAGAAGACCCAAGAGGTAAAGAAAAACAAAGATCCCAGTCCCCACAAGAAGCCCACGTTTGCTTACACGCTATGGCTG
AAGGCCAATCAAGAGAAGATCAAGGCAGATCACCCTGGCATCAGCACCACAGATCTTCCTAAGAAGGCAGACAAGATGTG
GAAGAGGATGTCCAAGAAGAAAGGGAAGTTGGGGCACGGGGGTAAGGATGAGGTCGCCAGCTGTGAATGTGAGAAAGCCA
CGAAAGAATGTGAAGGAGGCCCATGTAAGTCTTCTAAGAGGGACAAGGCAAAGACAAAGAAAGACAGAATAAAGATGGAC
AAGAAATCCCCTCCACCGAGGGGCTCCTCCTCCAAGTCATCATCCAGGCAGCTAAGTGAGAGCCTCGAGGGCAAAGACTC
TGTGCCCAGGGGAGAA

Alignment

ORF - retro_cpor_70 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.41 %
• Parental protein coverage: 94.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAETLEFNDIYQEVKGSMNDGRLRLSRQGIIFKNSKTGKVDNVQAGELTEGVWRRVALGHGLKLLTKNGH
          MAE.LEF.DIYQE.KGSM..G.LRL..QGIIF..SKTGKVDN.QA.EL.EGVWRRV.LGHGLKLL.K.GH
Retrocopy MAEMLEFSDIYQEMKGSMKEGHLRLDHQGIIFRHSKTGKVDNIQACELMEGVWRRVSLGHGLKLLLKHGH

Parental  VYKYDGFRESEFEKLSDFFKTHYRLELMEKDLCVKGWNWGTVKFGGQLLSFDIGDQPVFEIPLSNVSQCT
          VY.YDGF.ESEF..LS.FFKTHY.LEL.EKDLCVKGWNWGTVKFG.QLLSFDIG.Q.VFEIPLSNVSQCT
Retrocopy VYRYDGFQESEFQRLSHFFKTHYHLELKEKDLCVKGWNWGTVKFGEQLLSFDIGSQSVFEIPLSNVSQCT

Parental  TGKNEVTLEFHQNDDAEVSLMEVRFYVPPTQEDGVDPVEAFAQNVLSKADVIQATGDAICIFRELQCLTP
          T.KNEVTLEFHQ.DD.EVSL.E.RFYVPPTQE.GVD.V.AFAQNVLSKADVIQAT.DAICIF.ELQCLTP
Retrocopy TAKNEVTLEFHQSDDVEVSLVEMRFYVPPTQEEGVDLVQAFAQNVLSKADVIQATADAICIFQELQCLTP

Parental  RGRYDIRIYPTFLHLHGKTFDYKIPYTTVLRLFLLPHKDQRQMFFVISLDPPIKQGQTRYHFLILLFSKD
          RGRYDIRIYPTFLHLHGKTFDYKI....VL.LFLLPHKDQRQMFFVISLDPPIKQGQTRYHFLILLFSK.
Retrocopy RGRYDIRIYPTFLHLHGKTFDYKISFSMVLHLFLLPHKDQRQMFFVISLDPPIKQGQTRYHFLILLFSKE

Parental  EDISLTLNMSEEEVEKRFEGRLTKNMSGSLYEMVSRVMKALVNRKITVPGNFQGHSGAQCITCSYKASSG
          E.I.LTLNM.EEEVEKRFEG.LTK.M.GS.YE..SRVMKALVN.KITVPGNFQGH.GA.CI.CSYKASSG
Retrocopy ENITLTLNMNEEEVEKRFEGQLTKTMVGSRYEVFSRVMKALVNHKITVPGNFQGHLGAKCIACSYKASSG

Parental  LLYPLERGFIYVHKPPVHIRFDEISFVNFARGTTTTRSFDFEIETKQGTQYTFSSIEREEYGKLFDFVNA
          LLYPLE..FIYVHKPPVH..F.EI..VNFARG.TTTR.FD.EIETKQGTQ.TFSSI..EEYGKLFDF..A
Retrocopy LLYPLEQDFIYVHKPPVHVHFHEIACVNFARGITTTRFFDLEIETKQGTQFTFSSIQKEEYGKLFDFISA

Parental  KKLNIKNRGLKEGMNPSYDEYADSDEDQHDAYLERMKEEGKIREENANDSSDDSGEETDESFNPG-EEEE
          KKLNIKN..LK.G.NP.Y..Y.DSDE..HDAYLERMKEEGKIREEN.NDSSDD.GEE.DESF.PG.EEEE
Retrocopy KKLNIKNQELKDGKNPKYRKYTDSDEELHDAYLERMKEEGKIREENPNDSSDDLGEEMDESFKPGEEEEE

Parental  DVAEEFDSNASASSS-SNEGDSDREEKKRKQLKRAKMTKDRKSRKKTVEAKKGKDPNAPKRPMSAYMLWL
          .VAEEFDSNAS..SS.SNEGDSD..EK..KQL.RAK..KD.K..KKT.E.KK.KDP...K.P..AY.LWL
Retrocopy EVAEEFDSNASTTSSFSNEGDSDQDEKEQKQLQRAKTAKDHKDHKKTQEVKKNKDPSPHKKPTFAYTLWL

Parental  NASREKIKSDHPGISITDLSKKAGEIWKGMSKEK-KEEWDRKAEDARREYEKAMKEYEGGRGESSKRDKS
          .A..EKIK.DHPGIS.TDL.KKA...WK.MSK.K.K.....K.E.A..E.EKA.KE.EGG...SSKRDK.
Retrocopy KANQEKIKADHPGISTTDLPKKADKMWKRMSKKKGKLGHGGKDEVASCECEKATKECEGGPCKSSKRDKA

Parental  KKKKKVKAKMDKKSTPSRGSSSKSSSRQLSESFKSKEFVSSDE
          K.KK....KMDKKS.P.RGSSSKSSSRQLSES...K..V...E
Retrocopy KTKKD-RIKMDKKSPPPRGSSSKSSSRQLSESLEGKDSVPRGE

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	51.53 RPM
SRP017611_kidney	0.00 RPM	59.36 RPM
SRP017611_liver	0.00 RPM	30.99 RPM
SRP040447_lung	0.00 RPM	91.12 RPM
SRP040447_skeletal_muscle	0.14 RPM	44.90 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_70 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_70 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000375	1 retrocopy	retro_btau_1834,
Cavia porcellus	ENSCPOG00000000480	1 retrocopy	retro_cpor_70 ,
Equus caballus	ENSECAG00000016612	1 retrocopy	retro_ecab_516,