RetrogeneDB ID: retro_vpac_536

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_3526:58423..59895(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSVPAG00000002765
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:HGNC Symbol;Acc:20219]

Sequence

>retro_vpac_536
ATGGCAGACAAGCAGCACCGTGTGAAAGTCTATATGATGAGTGATGACCAACTATGGGATGAGCTAGGCACGGGGTACCT
CTTATCCACTTACGTGGAGCGGCTTCAGGGCCTGTCTCTGCTAGTTCAATCGGAGTCCGATGGTTCACTGATCTTGGAGT
CAAAGATAAATCCGAACACGCCCTATCAGAGAAAACGAGAGAACCTGATTATTTGGTATGAAGCTGAGAACCATGGTATA
GCAATAATTTTCCAGGACCCAGCAAGTTGTTACGAGATCTGGAAAGACATTTGCAAGGTTCAAGGTAAAGACCCATCTGT
CGAAATCACAGAAGACCTCTTGGATGAATCCGAAGAAGAACAATGTGATGACTTGCCGGAAACCTCTGAACAGCTTGGCC
TACCAAACTTTGAACTCAGTAAACTTGAACAGATTGCTGCCTTAGTTACTGCGGGTCTCACCTCACGTTTGCGTAAGGAA
AGGCTGGCTCTGGTCTTGGAAAATGAGAACTATATTAAAAAGCTACTGCAGTTGTTTCACACCTGTGAGAACCTAGAGGA
TACTCAAGGCTTACACTATTTGCATGAAATTATTAAAGGAATCTTATGTCTCAACAAGAAATCTCTGTGTGAGATCCTGT
TTTCTGATGAATATATCATGGATGTGGTGGGATGCCTTGAACATGAACCTACTTTGGCTCAGCCAAGAAGGCATAGGGAA
TTCTTAACCCAAAATGCCAAGTTCAAGGAAGTTATACCAATAACAAACTGTGAACTTCGGCAAAAAATACATCAGACATA
CAGGGTACAGTACATTCATGACATCCTCGTGTCTAAACCATCCGTGTTTAAAGAGAATCTTTTTTCTACTATTACAACTT
TTATTTTTTTAAACAAGGTTGAGATAGTCAGCATGCTGCAGGAAGATGACAAGTTTTTGGCTGAAGGTTTTGCACAGTTA
AGGGATAAGACCACAGATATTGATAAACGGCGTGAACTGGTGTTTTTTTTCAAGGAATTCTGTGCATTTTCTCGAACGTT
ACAGCCTCAAAGCAAGAATACCTTATTCAAAACATTGACACAACTGGGAATTCTTCCTGCTCTTAAAATTGTAATGGCCA
TGGATGATTTGCAGATAAAATCAGCTGCTACTGATATATTTGCTTATCTAGTAGAGTATTGTCCATCCATAATCCGAGGA
TTTATAATGGAAGAAGCCCAGCAGAGTGAAGATGGCAACCTCTTCATTAATTTAGTAATTGAACAAATGATCTGTGATAC
TGATCCTGAGCTCGGAGTGCTTTTCATTTAATGGAACTTCTCCGAGAGCTACTTGATCCAGACAACATGCTGGCAACACC
TACTAAATGTGAAAGAAGTGAATTTCTAAATTTCTTTTATAAACGTTGTATGCATAACTTAATTATACCGCTTTTGTCAA
CCACTTCAGAAGATGTATGTGAAGAAGATAAC

Alignment

ORF - retro_vpac_536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.21 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDTRRRVKVYTLNEDRQWDDRGTGHVSSGYVERLKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
          M.D...RVKVY....D..WD..GTG...S.YVERL.G.SLLV..ESDGSL.LESKINPNT.YQ.....LI
Retrocopy MADKQHRVKVYMMSDDQLWDELGTGYLLSTYVERLQGLSLLVQSESDGSLILESKINPNTPYQRKRENLI

Parental  VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEEERFDDM--SSPGLELPSCELS
          .W.EAEN...A..FQ..A.C.EIW..IC.VQGKDPSV.IT.DL.DESEEE..DD....S..L.LP..ELS
Retrocopy IWYEAENHGIAIIFQDPASCYEIWKDICKVQGKDPSVEITEDLLDESEEEQCDDLPETSEQLGLPNFELS

Parental  RLEEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALF
          .LE.IA.LV...L.S.LR.E.LAL.LENE.YIKKLL.LFH.CE.LE...GLH.L.EIIKGI..LN...L.
Retrocopy KLEQIAALVTAGLTSRLRKERLALVLENENYIKKLLQLFHTCENLEDTQGLHYLHEIIKGILCLNKKSLC

Parental  EVMFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTP
          E..FS.E.IMDV.GCLE..P.L.QPR.HREFLT..AKFKEVIPI...EL.QKIHQTYRVQYI.D.....P
Retrocopy EILFSDEYIMDVVGCLEHEPTLAQPRRHREFLTQNAKFKEVIPITNCELRQKIHQTYRVQYIHDILVSKP

Parental  SVFEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQ
          SVF.EN..ST...FIF.NKVEIV.MLQED.KFL...FAQL.D..TD..KR.ELV...KEFCAFS.TLQPQ
Retrocopy SVFKENLFSTITTFIFLNKVEIVSMLQEDDKFLAEGFAQLRDKTTDIDKRRELVXXXKEFCAFSRTLQPQ

Parental  NRDAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVEYNPSMVREFVMQEAQQNDDDILLINLII
          .....FKTL...GILPAL.....MDD.Q..SAATDIF.YLVEY.PS..R.F.M.EAQQ..D..L.INL.I
Retrocopy SKNTLFKTLTQLGILPALKIVMAMDDLQIKSAATDIFAYLVEYCPSIIRGFIMEEAQQSEDGNLFINLVI

Parental  EHMICDTDPELG-GAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSK
          E.MICDTDPELG..A..LM.LLR.L.DP.NMLAT..K.E..EFL.FFYK.CMH.L..PLL..T.ED....
Retrocopy EQMICDTDPELG<SAFHLMELLRELLDPDNMLATPTKCERSEFLNFFYKRCMHNLIIPLLSTTSEDVCEE

Parental  DD
          D.
Retrocopy DN

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_536 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_536 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536 ,