RetrogeneDB ID: retro_vpac_635

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_8751:6492..8682(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF532
• Ensembl ID: ENSVPAG00000008243
• Aliases: None
• Description: zinc finger protein 532 [Source:HGNC Symbol;Acc:30940]

Sequence

>retro_vpac_635
GAGCTGATGCCCAAATAGGTTATGATCAAGCCTGTGATGACCACATTCCTCCTGGTGTCAGCTGTGAAGATGGCTGCTCG
CAAGTCATTAATGTGAAGCTCACCAACAACACAATGGTGAAAGACACTGTCATATCTGCTGCCTTCATTCAGAGCACCAG
CAGCGCCATCATTAAAAGCCGCCAATGCCACCCAGCAGCAAACTGTCTTTGTGCCGGGCTCCAGCCTGGCCAATGCCAAA
CTTGTGCCAAAGACTCTGCACCTTGCCAACTTAACCTTCTGCCTCAAGGCACTCAGGCCATGTCTGAGCTCTGCCAAGTG
CTCACCACACCTCAGCAGCAAATAAAGCAGGTAATAATCAATGCCGTGGCCTCGCAGCCACCCAAAAAGTTGTCATGGGT
CCAGGTGGTGTCCTCCCTGCAGAGTTCTGTGATGGAAGCTTTCACCAAGGTGCTGCGCAGCATCAGCCCAGTCCCAGCTT
ACATCCCCAACCTCAGTCCTCCTGCCAACACGAGCATCACATTATAAACCCGTGGGTACAAGTGCTTGGAGTATGGGGAC
TCCTTTGCCCTGGAAAGAGCCTGACCCAACACTAAGACAGATGCAGTGTGTGCACTGAAGTAACATGCAACCACTGTAGT
AAGAACCTGATTACTGACAACAAGTGAAGCCTCCTGTCCCATGCCCGTGGGCACAAGGAGAAGGGAGAGGTGATGCAGGG
CTCCCACTTGATTGTGAAGCCGGTCCCAGGAGATCAAATGATCGTTTCTTCATCAAGCAGTATCCTGCTTCATCTTCCAC
TCTCCTGAGCTCCGTGGGGCCAGCACACACACTGTAACATAAATTCAGTCTGGCAAAGTGGGACAGTCACATCAGCCCCT
TAAGGCACAGCCATCCTTCCAGCTATGCCTCGGGATGAAGACCCATCCAAGCTCTGTAGGCATAGTCTGAAATGTTTGCA
GTGAAATGAAGTTTTCCAGGATGAGACATGGCTGGCTACCCACGTCCAGCAGGCTGCAGACAGCAGTGGACAAAAGACTT
GCACTGTCTGCCAGATGCTGTTTCCTAACCCGTGCAGCTCTGCCTCCCACCAGAGAATCCATCAGCACAAATCTCCCTGC
GCCTGCCCCGAGTGCAGGGCCATCTGCAGCTTGGTGCACTTCCAGACCCACGTCACCAAGAACTGTCTACACTACATGTG
AGAGTTGGTTTTCGATGTTCATATTGCAATGTTGTCTCCTCTGACATGGCCACGCTGAAGTCTCACACTCAAGTTTCTCA
CTGTGAAGTCTTCTACAAGTGTCCTGTCTCTCCAGTGGCATTTAAGTCTGCCCCAAGTGCACATTCACATGTGTAGACAC
AGCACCCCGGCATCAGGATCAGAGAGCCAAGAATAATATATAAGTGTTCCATGTTCGACACTGTATTCACCCTGCAAATC
CTGCCGTATCGCCACTTTGACCAGCACGTTGAAAACCAGGTGTCTGTTTTCAAGTGTCTAGACTGTTCTCTTTTACATGC
ACAGAAGCAACTCATGATGAACCATATCAAGTCTATGCGTGGAACACTGAAAAGCATGGAAGGGCCTCCAAACTTGGGTA
TAGACTTGCCTTTGAGCATTAAGCCTGGAATTCAAAATTCAGCAAATCAAAACACAGAAGACACCAGATCCATGAATGGG
AAAGAGAAATTGGAAAAGAAATCCCCATCACCTGCGAAGAAATCAGTGGAAAAAAAAAAAGTGGCTAGTCCTGGGTGAAT
GTGTTGAGGGTGTGACCACCTGTTCACACAGAGAGACGTTAACATTTCCCTCATGAGGAAGGAGCATGGGAAGCAAATGA
AGAATCACCCCTGTCACCAGTGTGAAAAATCTTTCAGCTCATCCCTCAGCCTCTGCCATCACAACCAGGTCAAACACAAA
GGCATCAGGAAAGTTTACACCTACTCACACTGCCCAGACTCCAGATGGACCTTCATGAAATGACTGATGCTGGAGAAACA
TATCCAGCTCACACATGATATTAAGGATCCTGACTTGAAAGGAAAGACAGAAGCCACCAATGTGTAGGAAATGGAAATAA
AAGAAGATGCCAAGATTCCCAGCCCCAAGTGGAAGATAGAAGAACCTGTTCTAGAGTTCAGACTGCCTAGAGGATCCATC
ACCCGACCCCTGAGGAAGCTGAAGACAAAC

Alignment

ORF - retro_vpac_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.14 %
• Parental protein coverage: 83.68 %
• Number of stop codons detected: 12
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  KVFPKQSQIQPVATAFLPVSAVKTAG-SQVINLKLANNTTVKATVISAASVQSASSAIIK-AANAIQQQT
          ...PK...I.PV.T.FL.VSAVK.A..SQVIN.KL.NNT.VK.TVISAA..QS.SSAIIK.AANA.QQQT
Retrocopy ELMPK*VMIKPVMTTFLLVSAVKMAA<SQVINVKLTNNTMVKDTVISAAFIQSTSSAIIK>AANATQQQT

Parental  VVVPASSLANAKLVPKTVHLANL-NLLPQGAQATSELRQVLTKPQQQIKQAIINAAASQPPKKVSRVQVV
          V.VP.SSLANAKLVPKT.HLANL.NLLPQG.QA.SEL.QVLT.PQQQIKQ.IINA.ASQPPKK.S.VQVV
Retrocopy VFVPGSSLANAKLVPKTLHLANL<NLLPQGTQAMSELCQVLTTPQQQIKQVIINAVASQPPKKLSWVQVV

Parental  SSLQSSVVEAFNKVLSSVNPVPVYIPNLSPPANAGITLPTRGYKCLECGDSFALE-KSLTQHYDRRSVRI
          SSLQSSV.EAF.KVL.S..PVP.YIPNLSPPAN..ITL.TRGYKCLE.GDSFALE.KSLTQH.DR.SV..
Retrocopy SSLQSSVMEAFTKVLRSISPVPAYIPNLSPPANTSITL*TRGYKCLEYGDSFALE<KSLTQH*DRCSVCT

Parental  EVTCNHCTKNLVFYNKCSLLSHARGHKEKGVVMQCSHLILKPVPADQMIVSPSSNT-PASSSALPSSVG-
          EVTCNHC.KNL...NK.SLLSHARGHKEKG.VMQ.SHLI.KPVP.DQMIVS.SS...PASSS.L.SSVG.
Retrocopy EVTCNHCSKNLITDNK*SLLSHARGHKEKGEVMQGSHLIVKPVPGDQMIVSSSSSI<PASSSTLLSSVG<

Parental  AGTHTVTKIQSGI-TGTVISAPSSTPIIPAMPLDEDPSKLCRHSLKCLECNEVFQDETSLATHFQQAADT
          A.THTVT.IQSG...GTV.SAP..T.I.PAMP.DEDPSKLCRHSLKCL..NEVFQDET.LATH.QQAAD.
Retrocopy ASTHTVT*IQSGK<SGTVTSAP*GTAILPAMPRDEDPSKLCRHSLKCLQ*NEVFQDETWLATHVQQAADS

Parental  SGQKTCTVCQMLLPNQCSYASHQRIHQHKSPYTCPECGAICRSVHFQTHVTKNCLHYT-RRVGFRCVHCN
          SGQKTCTVCQML.PN.CS.ASHQRIHQHKSP..CPEC.AIC..VHFQTHVTKNCLHY...RVGFRC..CN
Retrocopy SGQKTCTVCQMLFPNPCSSASHQRIHQHKSPCACPECRAICSLVHFQTHVTKNCLHYM<VRVGFRCSYCN

Parental  VVYSDVAALKSHIQGSHCEVFYKCPICPMAFKSAPSTHSHAYTQHPGIKIGEPKIIYKCSMCDTVFTLQT
          VV.SD.A.LKSH.Q.SHCEVFYKCP..P.AFKSAPS.HSH..TQHPGI.I.EP.IIYKCSM.DTVFTLQ.
Retrocopy VVSSDMATLKSHTQVSHCEVFYKCPVSPVAFKSAPSAHSHV*TQHPGIRIREPRIIYKCSMFDTVFTLQI

Parental  LLYRHFDQHIENQKVSVFKCPDCSLLYAQKQLMMDHIKSMHGTLKSIEGPPNLGINLPLSIKPTTQNSAN
          L.YRHFDQH.ENQ.VSVFKC.DCSLL.AQKQLMM.HIKSM.GTLKS.EGPPNLGI.LPLSIKP..QNSAN
Retrocopy LPYRHFDQHVENQ-VSVFKCLDCSLLHAQKQLMMNHIKSMRGTLKSMEGPPNLGIDLPLSIKPGIQNSAN

Parental  QNKEDTRSMNGKEKLEKKSPSPVKKSVEPKKVASPGWTCWECDRLFTQRDVYISHVRKEHGKQMKKHPCR
          QN.EDTRSMNGKEKLEKKSPSP.KKSV....VASPG..C..CD.LFTQRDV.IS..RKEHGKQMK.HPC.
Retrocopy QNTEDTRSMNGKEKLEKKSPSPAKKSVXXXXVASPG*MC*GCDHLFTQRDVNISLMRKEHGKQMKNHPCH

Parental  QCDKSFSSSHSLCRHNRIKHKGIRKVYTCSHCPDSRRTFTKRLMLEKHIQLMHGIKDPDLKEMTDATNEE
          QC.KSFSSS.SLC.HN..KHKGIRKVYT.SHCPDSR.TF.K.LMLEKHIQL.H.IKDPDLK..T.ATN..
Retrocopy QCEKSFSSSLSLCHHNQVKHKGIRKVYTYSHCPDSRWTFMK*LMLEKHIQLTHDIKDPDLKGKTEATNV*

Parental  ETEIKEDAKVPSPKRKLEEPVLEFRPPRGAITQPLKKLKIN
          E.EIKEDAK.PSPK.K.EEPVLEFR.PRG.IT.PL.KLK.N
Retrocopy EMEIKEDAKIPSPKWKIEEPVLEFRLPRGSITRPLRKLKTN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_635 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_635 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000008341	2 retrocopies	retro_nleu_3013, retro_nleu_581,
Pan troglodytes	ENSPTRG00000039047	1 retrocopy	retro_ptro_1726,
Vicugna pacos	ENSVPAG00000008243	2 retrocopies	retro_vpac_454, retro_vpac_635 ,