RetrogeneDB ID: retro_cjac_1429

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:87982278..87984182(-)
• Located in intron of: ENSCJAG00000020142

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H14
• Ensembl ID: ENSCJAG00000017345
• Aliases: None
• Description: zinc finger CCCH-type containing 14 [Source:HGNC Symbol;Acc:20509]

Sequence

>retro_cjac_1429
ATGGAGATCGGACCGAGATCAGCCACAAGATCCAGAGTCCCATTAAGGGGAAATTGCAAGAATTAGGAGCTTATGTTGAT
GGAAAACTTCCTGATTACATTATGGTGATGGTGGCCAACAAGAAAAGTCAGGACCAAAAGACAGAGGATCTCTCCCTGTT
TCTAGGGAACAACACAATTGGATTCACCGTATGGCTTCATAGTGTATTAGAAAAACTTTGCTCTGTTACAACTGAACCTT
CTAGTCTAAAGTCTTCTGATACCAACGTCTTTGATAGCAACGTGCCTTCAAACAAGAGCAGGTTCAGCCGGCGAGATGAG
AGGCGGCATGAAGCTGAAGTGCCACCACTTGCCGTTCCTGGCACTAGACCTGAAACAAGAGATTCCAGAGTTTCTACAAG
TTCACAGCATCAAAAAGCACTAATGTCAGGCAGCCCTATGACGACGGAGCTGCAACCCGACTAATGTCAACAGTGAAAAC
TTTGAGGGAGGCAGCGCCCTCTGAAGTTGTGATTGATATGAAGCCAGAACCAGATGATCTCATTGACGAAGACCTGAACT
TTGTGCAGGAGAACACTTTATCTCAGAAAAAACCTACAGTGACACTTACATCTGGTTCTTCTCGCCCTTCTATGGAAATT
TCTCAACCACCTGCAAGTAGAAATGCAGACAGTGGTGTTCATTTAAACAGGTTGCAATTTCAACAGCAGCAAAATAATAT
TCATGCTGCCAAGCAGCTTGATATACAGAACAGTTGGGCATATGAAACAGGACGTTTGTGGGAACCAGAAGTGCTTAACA
GCTTAGAAGAAACATATAGTCCGTTCTTTAGAAACAACTGGGAGAAGATGAGCATGGAGGATGAAAACTTTCGGAAGAGA
AAGTTGCCTGTGGTAAGCTCAATTGTTAAAGTAAAAAAATTCAATCACGATGGAGAAGAGGAGGAGGAAGATAATGACTG
TGGGTCTCAAACAGGAAGCATCTCCAGCAGTGTGTCTATGCCAGCAAAGCCTGAAAGGAGACCTTCTCCTCCACCTTCTA
AACAAGCTAACAAGAATCGGATTCTGAAGGCTCGATCTGAAACTCAAGGATCCGTAACAAAAACAATGACTACTGCACAG
TCCCGCAGAAACAGACACTTCCAGCTGCTCCCAGAACTCCAACTTCTCAAGAAGAATTGCTGGCAGAAGAGGTCCAGGGA
CAAAGTAGGACCCCCAGAATAAGTCCCCCTATTAAAGAACAGGAAACAAAAGGAGATTCCGTAGAAAAAAATCAAGGAAT
TCAACAGAGGCAATTATTATCCAGACTACAAATGGACCCAATAATGGCAGAAACTCTGCGGATCGGTCGAGATTACTATG
TCATGGAATCCATGGTCCATGCAGACACAAGATGATTTATTCTGAAAAGCCAAAGGTGTCCTACAAAATAGTAGTGGCAC
CAAACCAAGAGTCAGGGATGGAGACTGCAGATTCCCTTCGGGTACTTTCAGGACACCTTATGCAGCCACGAGATCTTGTA
CAACCAGATAAACCTGCAAGTCCCAAGTGTATAGTGACACTGGATGGTGTCCCCAACCCCCCAGGATACACGTCAGATCA
AGAGGAGGACATGCGCTTTGAAGGAATAAAACCTGTAAACCAAACTGCAGCCTCAAACAAGGGACTCAGAGGTCTCCTCC
ACCCACAGCACTTGCACTTGCTGAGCAGGCAGCCTGAGGACCCAAATGGTAGCTTTTCCAACGCTGAGATGAGTGAACTG
AGTATGGCACAGAAACCAGAAAAACTTTTGGAGCACTGCAAGTACTGGCCTGCTTGTCAAAACGGGGATGTGTGCACCTA
ACACCACCCCATCCCACCCTGCAAAGCCTTCCCCAATTGTAAGTTTGCTGAAAAATGTTTGTTC

Alignment

ORF - retro_cjac_1429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 86.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEIG-TEISRKIRSAIKGKLQELGAYIDEELPDYIMVMVANKKSQDQMTEDLSLFLGNNTVRFTVWLHGV
          MEIG.TEIS.KI.S.IKGKLQELGAY.D..LPDYIMVMVANKKSQDQ.TEDLSLFLGNNT..FTVWLH.V
Retrocopy MEIG<TEISHKIQSPIKGKLQELGAYVDGKLPDYIMVMVANKKSQDQKTEDLSLFLGNNTIGFTVWLHSV

Parental  LDKLRSVTTVQNPCGLKSSDTNIFDSNVSSNKSSFSRGDERRHEAAVPPLAIPSTRPEKRDSRVSTSSQE
          L.KL.SVTT...P..L.............SNKS.FSR.DERRHEA.VPPLA.P.TRPE.RDSRVSTSSQ.
Retrocopy LEKLCSVTT--EPSSLXXXXXXXXXXXXPSNKSRFSRRDERRHEAEVPPLAVPGTRPETRDSRVSTSSQH

Parental  -SKTTNVRQTYDDGAATRLMSTVKPLREPAPSEDVIDIKPEPDDLIDEDLNFVQENPLSQKKPTVTLTYG
          .SK.TNVRQ.YDDGAATRLMSTVK.LRE.APSE.VID.KPEPDDLIDEDLNFVQEN.LSQKKPTVTLT.G
Retrocopy <SKSTNVRQPYDDGAATRLMSTVKTLREAAPSEVVIDMKPEPDDLIDEDLNFVQENTLSQKKPTVTLTSG

Parental  SSRPSIEIYRPPASRNADSGVHLNRLQFQQQQNSIHAAKQLDIQTSWVYETGRLCEPEVLNSLEETYSPF
          SSRPS.EI..PPASRNADSGVHLNRLQFQQQQN.IHAAKQLDIQ.SW.YETGRL.EPEVLNSLEETYSPF
Retrocopy SSRPSMEISQPPASRNADSGVHLNRLQFQQQQNNIHAAKQLDIQNSWAYETGRLWEPEVLNSLEETYSPF

Parental  FRNNSEKMSMEDENFRKRKLPVVSSVVKVKKFNHDGEEEEDDDDFGSRTGSISSSVSVPAKPERRPSLPP
          FRNN.EKMSMEDENFRKRKLPVVSS.VKVKKFNHDGEEEE.D.D.GS.TGSISSSVS.PAKPERRPS.PP
Retrocopy FRNNWEKMSMEDENFRKRKLPVVSSIVKVKKFNHDGEEEEEDNDCGSQTGSISSSVSMPAKPERRPSPPP

Parental  SKQANKNLILKAISEAQESVTKT-TNYSTVPQKQTLPVAPRTRTSQEELLAEVVQGQSRTPRISPPIKEE
          SKQANKN.ILKA.SE.Q.SVTKT...Y.TVPQKQTLP.APRT.TSQEELLAE.VQGQSRTPRISPPIKE.
Retrocopy SKQANKNRILKARSETQGSVTKT<NDYCTVPQKQTLPAAPRTPTSQEELLAEEVQGQSRTPRISPPIKEQ

Parental  ETKGDSTEKNQGNNRRQLLCRLQIDPVMAETLQISWDYYDMESMVHADTRSFILK-KPKLSEEIVVAPNQ
          ETKGDS.EKNQG...RQLL.RLQ.DP.MAETL.I..DYY.MESMVHADTR.FILK.KPK.S..IVVAPNQ
Retrocopy ETKGDSVEKNQGIQQRQLLSRLQMDPIMAETLRIGRDYYVMESMVHADTR*FILK<KPKVSYKIVVAPNQ

Parental  ESGMKTADSLRVLSGHLMQTRDLVQPDKPASPKFIVTLDGVPSPPGYMSDQEEDMCFEGMKPVNQTAASN
          ESGM.TADSLRVLSGHLMQ.RDLVQPDKPASPK.IVTLDGVP.PPGY.SDQEEDM.FEG.KPVNQTAASN
Retrocopy ESGMETADSLRVLSGHLMQPRDLVQPDKPASPKCIVTLDGVPNPPGYTSDQEEDMRFEGIKPVNQTAASN

Parental  KGLRGLLHPQQLQLLSRQLEDPNGSFSNAEMSELSVAQKPEKLLERCKYWPACKNGDECAYHHPISPCKA
          KGLRGLLHPQ.L.LLSRQ.EDPNGSFSNAEMSELS.AQKPEKLLE.CKYWPAC.NGD.C..HHPI.PCKA
Retrocopy KGLRGLLHPQHLHLLSRQPEDPNGSFSNAEMSELSMAQKPEKLLEHCKYWPACQNGDVCT*HHPIPPCKA

Parental  FPNCKFAEKCLF
          FPNCKFAEKCLF
Retrocopy FPNCKFAEKCLF

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
SRP051959_colon	0.13 RPM	32.82 RPM
SRP051959_heart	0.25 RPM	41.04 RPM
SRP051959_kidney	0.24 RPM	53.98 RPM
SRP051959_liver	0.11 RPM	26.08 RPM
SRP051959_lung	0.41 RPM	51.99 RPM
SRP051959_lymph_node	0.27 RPM	34.20 RPM
SRP051959_skeletal_muscle	0.11 RPM	22.73 RPM
SRP051959_spleen	0.29 RPM	41.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1429 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030453	1 retrocopy	retro_btau_331,
Callithrix jacchus	ENSCJAG00000017345	1 retrocopy	retro_cjac_1429 ,
Felis catus	ENSFCAG00000012898	1 retrocopy	retro_fcat_966,
Mus musculus	ENSMUSG00000021012	1 retrocopy	retro_mmus_2181,
Otolemur garnettii	ENSOGAG00000005373	1 retrocopy	retro_ogar_2910,