RetrogeneDB ID: retro_cpor_57

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_21:14041342..14044657(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000005398
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSCPOG00000004827
• Aliases: None
• Description: None

Sequence

>retro_cpor_57
ATGGCGGCGGCCGGTTCTGTAGGAGTACCGGGGACCGTGTCGGAAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
AAACCCAAGCTGTATGGTGCGGAGGCAAGCAGAGGAAATCTATGAAAACATACCAGGTCTGTGTAAGACTACCTTTCTAT
TAGATGCAGTCAGAAACAGAAGAGTAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGTTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAGGTCTATCCAAATCTGCCTTTTGATGTTCAGAGGGATGTCAAGATTGAACTGATACTGGCTGTTAAGTT
AGAAACACATACTAGCATGAGGAAAAAGCTTTGTGATATTTTTGCTGTGCTGGCTAGGAATTTGATAGATGAGGATGGCA
CTAATCATTGGCCAGAAGGTCTGAAGTTCCTTATTGATTCGATCTACTCTAAAAATGTAGTTCTATGGGAAGTTGCACTT
CATGTCTTCTGGCACTTTCCTGGGATTTTTGGGAACCAAGATCGACACGATTTGGATATCATCAAAAGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCTGCTAGAGCTGCAGCTGCATTCGTACTTGCTAATGAAA
ATAATATTGCACTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGATTCATGCTACCAGGAT
GATGATTCAGTACTAGAGTCTCTTGTTGAGATTGCAGATACTGTACCTAAGTACTTGGGTCCTTATATAGAAGATACTCT
ACAATTGAGCCTGAAGTTATGTGGAGACTCTAGACTTAGTAATCTACAACGCCAGTTGGCTCTTGAAGTGATAGTAACCT
TGTCTGAAACTGCAACTCCAATGTTGAAAAAACATACAAATATTATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGAGCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCGCTAGACAGGCTGGCTTGTGGGCTTGGTGGAAAAATTGTTTTACCAATGACCAAAGAGCATATCATGCAAA
TGCTTCAGAGCCCTGACTGGAAATGTCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGTTGCCATCAGCAA
ATGGAACCAATTCTAGATGAAACAGTAAACTCTGTTTTGCTTTTTCTTCAGGATCCTCACCCAAGGGTGAGGGCTGCAGC
CTGTACTACTCTTGGACAGATGGCTACAGATTTTGCACCTAGTTTCCAAAAGAAATTCCATGAAACAGTGATTGCAGCTT
TATTACGTACTATGGAAAATCAAGGTAATCAGCGTGTGCAGTCTCATGCAGCTTCTGCCCTTATTATTTTTATTGAAGAC
TGTCCTAAATCACTGCTAGTTCTATATTTGGATGGTATGGTAAAAAATCTACATTCCATCTTGGTGATTAAACTTCAAGA
GCTGATTCGAAATGGTACTAAGTTGGCATTAGAACAACTTGTGACAACTATTGCCTCAGTTGCAGATACAATGGAAGAAA
AATTTGTTCCATATTATGATACATTTATGCCCTCACTAAGACACATTGTTGAGCTTGCTGTTCAGAAGGACCTCAAGACT
TTGAGAGGAAAGACTATTGAGTGCATTAGCCACGTTGGTCTTGCTGTTGGAAAGGAAAAATTTATGCAAGATATATCAAA
TGTGATGGAGCTATTGTTGAAGGCACAGTCAGACTTAAGTAATATAGAAGATGATGACCCTCAGACATCATATATGGTTT
CAGCATGGGCTAGAATGTGTAAAATTCTTGGAAAAGATTTTCAACAGTATCTTCCACTAGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTGGCTCTCTTAGATACACAAGATGTGGAGAATATGAGTGATGATGATGGTTGGCAATT
TGTAAATCTTGGAGATCAGCAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGTTGG
TTTACTACGCTAAGGAATTAAGAGAAGGATTTGTAGAATATACAGAACAAGTTGTTAAACTGATGATTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTAGCAGCAGCAGAGTCCATGCCTTTTCTCCTGGAATGTGCAAGAAGTCGTGGTCC
AGAGTATCTTTCACAGATGTGGAAGTTCATATGTGATCCCTTAATCAAAGCTATTGGGACCGAACCTGATACAGATGTAC
TTTCAGAAATAATGAATTCGTTTGCAAAATCCATTGAGGTCATGGGAGATGGTTGCCTTAATGATGAACACTTGGAAGAA
CTGGGAGGAATACTGAAAGCAAAACTTGAAGGACACTTTAAAAACCAAGAATTACGACAGGTTAAAAGACAAGAAGAAAA
CTATGATCAACAGGTTGAGATGTCTCTGCAAGATGAAGATGAGTGTGATGTTTACATTCTGACCAAAGTATCAGATATTT
TGCATTCATTATTTAGTACTTACAAGGAAAAGATTTTACCATGGTTTGAACAGCTACTTCCATTAATTGTAAATCTTATT
TGTTCAAATAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATATTTGATGATATCATAGAGCACTGCAGTCCAACTTC
ATTTAAATATGTGGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGACAACAACCCTGAAGTTAGGCAGGCTGCTG
CTTATGGCTTGGGTGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCTTTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTTATTGCTACAGAGAATTGCATCTCAGCAATAGGGAAAAT
TTTGAAGTTTAAGCCTAACTGTGTAAATGTAGACGAAGTTCTTCCACATTGGTTATCATGGCTTCCACTGCATGAAGACA
AAGAGGAAGCTATTCAGACTTTGAATTTTCTCTGTGACTTAATTGAAAGTAACCATCCAATTGTAATTGGCCCAAATAAT
TCCAATCTTCCCAAAATAATCAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAACTATGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTTGTTCGTCAGGTACAGAGTTCTGAAGAATTGTGGTTGGAATGCATATCCCACCTTGATGATGAAC
AGCAGGAAGCTCTGCAGGAGTTGATAAATTTTGCT

Alignment

ORF - retro_cpor_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.65 %
• Parental protein coverage: 63.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELLMIIQME
          E.YENIPG..K.TFLL.A.RN.....E.RQMAA.LLRRLLSS.F.EVYP.LP.DVQ...K.EL......E
Retrocopy EIYENIPGLCKTTFLLDAVRNRRVGYEVRQMAAALLRRLLSSGFEEVYPNLPFDVQRDVKIELILAVKLE

Parental  TQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLREAALHIFWNFPGIFGNQQQHYL
          T..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS..S.N..L.E.ALH.FW.FPGIFGNQ..H.L
Retrocopy THTSMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSIYSKNVVLWEVALHVFWHFPGIFGNQDRHDL

Parental  DVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFADLLPGFLQAVNDSCYQNDDSVLKSL
          D.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.ALFK.FADLLPG.LQAVNDSCYQ.DDSVL.SL
Retrocopy DIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIALFKDFADLLPGILQAVNDSCYQDDDSVLESL

Parental  VEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTNIVAQTIPQMLA
          VEIADTVPKYL.P..E.TLQLSLKLCGD..L.N.QRQLALEVIVTLSETA..ML.KHTNI.AQ..P..LA
Retrocopy VEIADTVPKYLGPYIEDTLQLSLKLCGDSRLSNLQRQLALEVIVTLSETATPMLKKHTNIIAQAVPHILA

Parental  MMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
          MMV.L..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGGK.VLPM.KEHIMQMLQ.PDWK.RHAGLM
Retrocopy MMVELQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGGKIVLPMTKEHIMQMLQSPDWKCRHAGLM

Parental  ALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
          ALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDFAP.FQKKFHE.VIAALL.TM
Retrocopy ALSAIGEGCHQQMEPILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDFAPSFQKKFHETVIAALLRTM

Parental  EDQGNQRVQAHAAAALINFTEDCPKTLLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVA
          E.QGNQRVQ.HAA.ALI.F.EDCPK.LL..YLD..VK.LHSI.V.KLQELI..GTKL.LEQ.VT.IASVA
Retrocopy ENQGNQRVQSHAASALIIFIEDCPKSLLVLYLDGMVKNLHSILVIKLQELIRNGTKLALEQLVTTIASVA

Parental  DTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTD
          DT.EEKFVPYYD.FMPSL.HIVE.AVQK.L..LRGKTIECIS..GLAVGKEKFMQD.S.VM.LLLK.Q.D
Retrocopy DTMEEKFVPYYDTFMPSLRHIVELAVQKDLKTLRGKTIECISHVGLAVGKEKFMQDISNVMELLLKAQSD

Parental  FNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEFV
          ....EDDDPQ.SYM.SAWARMCKILGK.FQQYLP.V..PL.KTAS.KP.VALLDTQD.ENMSDDDGW.FV
Retrocopy LSNIEDDDPQTSYMVSAWARMCKILGKDFQQYLPLVIEPLIKTASAKPDVALLDTQDVENMSDDDGWQFV

Parental  NLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYFHDDI
          NLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVKLM.PLLKFYFHD..
Retrocopy NLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQVVKLMIPLLKFYFHDNV

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	37.50 RPM	91.68 RPM
SRP017611_kidney	20.94 RPM	81.45 RPM
SRP017611_liver	10.62 RPM	61.68 RPM
SRP040447_lung	15.06 RPM	107.82 RPM
SRP040447_skeletal_muscle	13.60 RPM	356.55 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_57 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_57 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 21 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003784	1 retrocopy	retro_amel_3,
Bos taurus	ENSBTAG00000039374	1 retrocopy	retro_btau_104,
Canis familiaris	ENSCAFG00000005561	1 retrocopy	retro_cfam_452,
Choloepus hoffmanni	ENSCHOG00000006061	1 retrocopy	retro_chof_11,
Cavia porcellus	ENSCPOG00000004827	2 retrocopies	retro_cpor_265, retro_cpor_57 ,
Equus caballus	ENSECAG00000014808	1 retrocopy	retro_ecab_37,
Felis catus	ENSFCAG00000025657	1 retrocopy	retro_fcat_24,
Homo sapiens	ENSG00000065150	1 retrocopy	retro_hsap_57,
Gorilla gorilla	ENSGGOG00000008742	1 retrocopy	retro_ggor_47,
Loxodonta africana	ENSLAFG00000016190	1 retrocopy	retro_lafr_22,
Myotis lucifugus	ENSMLUG00000006500	1 retrocopy	retro_mluc_295,
Mus musculus	ENSMUSG00000030662	2 retrocopies	retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys	ENSNLEG00000007831	2 retrocopies	retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus	ENSOCUG00000003898	1 retrocopy	retro_ocun_143,
Otolemur garnettii	ENSOGAG00000007570	1 retrocopy	retro_ogar_169,
Pongo abelii	ENSPPYG00000005458	1 retrocopy	retro_pabe_172,
Pan troglodytes	ENSPTRG00000005984	2 retrocopies	retro_ptro_49, retro_ptro_745,
Pteropus vampyrus	ENSPVAG00000004516	1 retrocopy	retro_pvam_8,
Rattus norvegicus	ENSRNOG00000010989	1 retrocopy	retro_rnor_240,
Sus scrofa	ENSSSCG00000009509	1 retrocopy	retro_sscr_24,
Ictidomys tridecemlineatus	ENSSTOG00000011164	1 retrocopy	retro_itri_32,