RetrogeneDB ID: retro_cpor_477

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_163:1844636..1847441(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000023166
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP1B1
• Ensembl ID: ENSCPOG00000005293
• Aliases: None
• Description: None

Sequence

>retro_cpor_477
ATGACTGACTCCAAGTACTTCACAACCAATAAAAAGGGAGAAATCTTTGCATTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGGAAAGAGGCTGTGAAAAAAGTGATTGTTGCTACGACTGTGGGGAAGGATGTTAGCTCTCTCTTTCCGGATG
TAGTCAACTGTATGCAGACGGATAACCTGGAATTAAAGAAGCTCGTGTATCTGTACTTGACAAACTACGCCAAGAGTCAA
CCAGACATGGCCAGCATGGCTGTCAACAGTTTTGTGAAGGACTGTGAAGATCCCAATCCTTTGATTCGGGCCTTGGCAGT
CAGAACCATGGGGTGCATCCGGGTGGACAAGATTACAGAATATATTTGTGAGCCCCTTCGCAAGTGCTTGAAGGATGAAG
ATCCCTATGTTCGGAAAACAGCAGCAGTCTGTGTGGCAAAACTCCATGATATCAATGCCCAAATGGTGGAAGATCAGGGA
TTTCTCGATTCTCTGCGGGATCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAATGCTGAAGCAGGATTGTCTGAAAT
TAGTGAGTCTCACCCAAACAGCAACTTTCTCAATTTGAACCCACAGAACATTAATAAGCTACTGACAGCTCTGAATGAGT
GCACCGAGTGGGGCCAGATTTTCATCTTGGACTGCTTGTCTAACTATAACCCTAAAGATGACTGGGAAGCTCAGAGCATC
TGTGAGTGGGTAACTCCCGGTTATCCCATGCCAACTCAGCAGTGGTATTCTCAGCAATAAAAGTCCTAATGAAATTTCTG
GAATTGTTACCCAAGGACTCCGACTACTACAATATGCTGCTGAAGAAGTTAGCTCCTCCACTTGTTACTTTGCTGTCTGG
GGAGCCAGAAGTGCAGTATGTTGCCTTGAGGAACATCAACTTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAAA
TCAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATGTTAAACTAGAGAAGTTGCACATCATGATTCGCCTGGTGTCC
CAAGCTAACATTGCTCAGGTTTTAGCAGAGCTGAAGGAATATGCCACTGAGGTGGATGCTGACTTCGTTCGCAAAGCTGT
GAGGGCCATTGGACGATGTGCCATCAAGGTGGAACAATCTGCAGAGCACTGTGTAAGCACATTGCTTGACTTAATCCAGA
CCAAAGTAAATTATGTGGTCCAAGAGGCAATTGTTGTCATCAGGGATATCTTCCGCAAATATCCCAACAAGTATAAAAGT
ATTATTGCCACTCTGTGTGAGAACTTAGACACCTTGGATGAGCCAGATGCACGAGCAGCCATGATTTGGATCATGGGAGA
ATATGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAGAGTTTCTTGGAGGGTTTTCATGAAGAAAGTACCCAAGTCC
AGCTCATTCTGCTTACTGCCATAGTAAAGCTGTTTCTCAAGAAACCATCAGAAACACAAGAGCTCATCCAACAGGTCTTG
AGTTTGGCAACACAGGATTCCGATAATCCTGACCTCCGAGACCAGGGCTATATTTATTGGTGTCTTCTCTCAACTGACCC
CAGTGACAGCCAAAGAAGTAGTCTTGTCTGAGAAGCCACTAATCTCTGAGGAAACAGACCTTATTGAGCCAACTCTGCTG
GATGAACTGATATGTCACAATGGTTCCTTGGCCTCTGTGTATCATAAGCCTCCCAATGCTTTTGTGGGAGTCATGGGATT
CATCGCAAACACTTGCCAATTCATCATGGGAGCACTGATGCAGGTGACAGTCCTGTTGGCACCACCATTGCAAGCAACCT
GGAACAGCCTCAGGTTATCCCCTCTCAAGGTGACCTTCTTGGAGATCTTTTAAATCTTGACCTTGGTCCCCCCAGTCAAT
GTGCCACAGGTGTCCTCCATGCAGATGGGAGCAGTGGATCTCCTGGGAGGACTAGATAGTCTGGTCGGACAGTCCTTCAT
CCCATCATCACTGCCTGCAACCTTTGCTCCCTCACCGACTCCTGCCATAGTCAGCAGTGTTCTTAATGACCTGTTTGAAC
TCTCCATGGGGATAGGCATGGCGCCTGGTGGATACGTGGCTCCTAAGGCTGTCTGGCTACTTGGAGTAAAGGCCAAAGGC
TTGGAGATTTCAGGAACATTTACTCACCGCCAGGGGCACATCTATATGGAAATGAACTTCACCAACAAAGCTCTGCAGCA
TATGACAGACTTTGCAATCCAGCTTAACAAGAACAGCTTTGGTGTCATCCCAAGCACTCCTCTGGCCATCCATACACCAC
TGATGCCAAACCAAAGCATTGACGTCTCCCTGCCTCTCAACACCTTGGGCCCAGTCATGAAGATGGAACCTCTAAATAAC
TTGCAGGTGGCTGTTAGAAACAATATTGATGTCTTCTACTTTAGCTGCCTCATCCCACTCAATGTGCTTTTTGTAGAAGA
TGGCAAAATGGAGCGCCAAGTCTTCCTGGCAACATGGAAGGACATTCCCAATGAAAATGAACTCCAGTTTCAGATTAAGG
AATGTCATTTAAATGCTGACACTGTTTCCAGCAAATTGCAAAACAACAATGTTTATACTATTGCCAAGAGAAACGTGGAA
GGGCAGGACATGCTGTACCAGTCCCTAAAGCTCGCTAATGGCATTTGGATTTTGGCTGAGCTACGTATCCAGCCAGGAAA
CCCTAATTATACGCTGTCACTGAAATGTAGAGCTCCTGAAGTGTCTCAATACATCTATCAGGTCTACGATAGCATTTTGA
AAAAC

Alignment

ORF - retro_cpor_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVY
          MTDSKYFTT.KKGEIF.LKAELN..KKEK.KEAVKKVI...TVGKDVS.LFPDVVNCMQTDNLELKKLVY
Retrocopy MTDSKYFTTNKKGEIFALKAELNNEKKEKRKEAVKKVIVATTVGKDVSSLFPDVVNCMQTDNLELKKLVY

Parental  LYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYL.NYAKSQPDMA.MAVN.FVKDCEDPNPLIRALAVRTMGCIRVDKITEY.CEPLRKCLKDEDPYVRKT
Retrocopy LYLTNYAKSQPDMASMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYICEPLRKCLKDEDPYVRKT

Parental  AAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTA
          AAVCVAKLHDINAQ.VEDQGFLD.L.DLI.DSNPMVVANA.A.LSEI.ESHP.SN.L.LNPQ.INKLLTA
Retrocopy AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAEAGLSEISESHPNSNFLNLNPQNINKLLTA

Parental  LNECTEWGQIFILDCLANYTPKDDREAQSICERVTP-RLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGT
          LNECTEWGQIFILDCL.NY.PKDD.EAQSICE.VTP.RLSHANSAVV.SA.KVLMKF.E.L.KD.DYY..
Retrocopy LNECTEWGQIFILDCLSNYNPKDDWEAQSICEWVTP<RLSHANSAVVFSAIKVLMKFLELLPKDSDYYNM

Parental  LLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQA
          LLKKLAPPLVTLLS.EPE.QYVALRNINLIVQKRPEILK.E.KVFFVKYNDPIYVKLEKL.IMIRL.SQA
Retrocopy LLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLHIMIRLVSQA

Parental  NIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFR
          NIAQVLAELKEYATEVD.DFVRKAVRAIGRCAIKVEQSAE.CVSTLLDLIQTKVNYVVQEAIVVI.DIFR
Retrocopy NIAQVLAELKEYATEVDADFVRKAVRAIGRCAIKVEQSAEHCVSTLLDLIQTKVNYVVQEAIVVIRDIFR

Parental  KYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLQLLTAIV
          KYPNKY.S.IATLCENLD.LDEP.ARAAMIWI.GEYAERIDNADELLESFLEGFH.ESTQVQL.LLTAIV
Retrocopy KYPNKYKSIIATLCENLDTLDEPDARAAMIWIMGEYAERIDNADELLESFLEGFHEESTQVQLILLTAIV

Parental  KLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTD-PVAAKEVVLAEKPLISEETDLIEPT
          KLFLKKP.ETQEL.QQVLSLATQDSDNPDLRD.GYIYW.LLSTD.PV.AKEVVL.EKPLISEETDLIEPT
Retrocopy KLFLKKPSETQELIQQVLSLATQDSDNPDLRDQGYIYWCLLSTD>PVTAKEVVLSEKPLISEETDLIEPT

Parental  LLDELICYIGTLASVYHKPPSAFVEGGRGVV-HKSLPPRTASNESTESPETAPAGAPTAEQPDVIPTQGD
          LLDELIC..G.LASVYHKPP.AFV.G..G....K.LP....S.....SP......A...EQP.VIP.QGD
Retrocopy LLDELICHNGSLASVYHKPPNAFV-GVMGFI<RKHLPIHHGSTDAGDSP-VGTTIASNLEQPQVIPSQGD

Parental  LLGDLLNLDLG-PPVSGPPLTTSSVQMGAVDLLGGGLDSLIGDTNFGAPPPA--APARLGAPIGSGLSDL
          LLGDLLNLDLG.PPV..P.....S.QMGAVDLL.GGLDSL.G........PA..AP....A...S.L.DL
Retrocopy LLGDLLNLDLG>PPVNVPQVS--SMQMGAVDLL-GGLDSLVGQSFIPSSLPATFAPSPTPAIVSSVLNDL

Parental  FDLTSGVGTLSGSYVPPKAVWLPAMKAKGLEISGTFMRQVGSISMDLQLTNKALQVMTDFAIQFNRNSFG
          F.L..G.G...G.YV.PKAVWL...KAKGLEISGTF....G.I.M....TNKALQ.MTDFAIQ.N.NSFG
Retrocopy FELSMGIGMAPGGYVAPKAVWLLGVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQLNKNSFG

Parental  LAPAAPLQVHAPLSPNQTVEISLPLNTVGSVMKMDPLNNLQVAVKNNIDIFYFSTLYPLHILFVEDGKMD
          ..P..PL..H.PL.PNQ....SLPLNT.G.VMKM.PLNNLQVAV.NNID.FYFS.L.PL..LFVEDGKM.
Retrocopy VIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVRNNIDVFYFSCLIPLNVLFVEDGKME

Parental  RQMFLATWKDIPNENEAQFQIRDCSLNAEAVSTKLQNSNIFTIAKRNVEGQDMLYQSLKLTNGIWVLAEL
          RQ.FLATWKDIPNENE.QFQI..C.LNA..VS.KLQN.N..TIAKRNVEGQDMLYQSLKL.NGIW.LAEL
Retrocopy RQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLANGIWILAEL

Parental  RIQPGSPSFTLSLKCRAPEVSQHVYQAYETILKN
          RIQPG.P..TLSLKCRAPEVSQ..YQ.Y..ILKN
Retrocopy RIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN

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	1.15 RPM	94.50 RPM
SRP017611_kidney	1.57 RPM	85.63 RPM
SRP017611_liver	0.44 RPM	85.92 RPM
SRP040447_lung	0.30 RPM	103.30 RPM
SRP040447_skeletal_muscle	0.04 RPM	74.47 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_477 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_477 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005293	1 retrocopy	retro_cpor_477 ,
Macropus eugenii	ENSMEUG00000008438	1 retrocopy	retro_meug_1205,
Macaca mulatta	ENSMMUG00000021380	1 retrocopy	retro_mmul_2615,