RetrogeneDB ID: retro_vpac_190

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2649:252358..253271(-)
• Located in intron of: ENSVPAG00000002313

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSVPAG00000004889
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_vpac_190
GAGTATGATCATCAGGAAGAAGATCTCACAGTTGGGTAGAGGGAGGTGACAGGCATGAGCTAGGCATTAACTTCAGCTGG
GCTAAAAGGATGGCATCATCCTTTGAGAGTTCATGACCAAGCCACTGCCAGGCTCAGTGAAAGATGGTCAATGAGTCCTC
AGTAAGCTAGCCTCAGTTGGAGAATATTGGCAATTTTATTAAAGCTATTCAGGCTTATGGTATGAAGCCACATGACATAT
TTGAAGCAAATGGTCTTTTTGAGAATGGAAACATGACCCAGGTTCAGACTATCCTGGTGGTCCTAGCAGATCTGACTAAA
ACAAAAGGATTACATGCAACCATTGACATTGGAGTTAAGTATGCAGAAAAATAAAGTTGTTTTGATGAAGGAAAATTAAA
AGTTGGCCAAAGTATGATTGGTTTGCCAATGGGAACCAACAGATGTTCAAAGCCAAGCAGGCATGATAGCCTATGGAACT
GGAAAGCATCTTTATGATCCCAAAATGCAAACTGACAAACCTTTTCTGATCAGGCCATGATTAGTGTGCAGATAGGGGCC
AAAAAAGGAGCCAGCCAGGTGGGAGTGTTAGCACTGGGTACCCCAAGAGACAACTATGATCAGAATCTAACATTACAACC
AGTGGGCAGCTCGACAATTTCTCTACGGATGGGTACCAACAAAATCACTTCCCAGAAAGGAATGAGTGTGTAAAGCTTGG
GCAGCAAGTATATGATCTCAAATACTGTGCTGCTCCCACAGAACCTGTCATTCACAATGGAAGCCAAGGAACAGGAACAA
AAGGGTTGGAAATCAGTGGTAATGATTACCAGGCAGAATATGCAGATGAGTAACATGGCACGTACCACGATGCCTACCCC
AAAGATGACCAATATGGCGACCAAGGCACTGAT

Alignment

ORF - retro_vpac_190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 98.71 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KYDHQAEEDLRNWIEEVTGMS-IGTNF-QLGLKDGIILCELINKLQPGSVKK-VNESSLNWPQLENIGNF
          .YDHQ.EEDL.....EVTGMS..G.NF.QLG.KDGIIL.E...K..PGSVK..VNESS...PQLENIGNF
Retrocopy EYDHQ-EEDLTVG*REVTGMS<LGINF<QLG*KDGIIL*EFMTKPLPGSVKD>VNESSVS*PQLENIGNF

Parental  IKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLKA
          IKAIQAYGMKPHDIFEAN.LFENGNMTQVQT.LV.LA.L.KTKG.H.TIDIGVKYAEK....FDEGKLK.
Retrocopy IKAIQAYGMKPHDIFEANGLFENGNMTQVQTILVVLADLTKTKGLHATIDIGVKYAEK*SC-FDEGKLKV

Parental  GQSVIGLQMGTNKCA-SQAGMTAYGTRRHLYD-PKMQTDKPF-DQTTISLQMGTNKGASQAGMLAPGTRR
          GQS.IGL.MGTN.C..SQAGM.AYGT..HLYD.PK......F.DQ..IS.Q.G..KGASQ.G.LA.GT.R
Retrocopy GQSMIGLPMGTNRCS>SQAGMIAYGTGKHLYD>PKCKLTNLF>DQAMISVQIGAKKGASQVGVLALGTPR

Parental  DIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSV-YGLGRQVYDPKYCAAPTEPVIHNGSQGTGTNGSEI
          D.YDQ.LTLQPV..STISL.MGTNK..SQKGMSV...LG.QVYD.KYCAAPTEPVIHNGSQGTGT.G.EI
Retrocopy DNYDQNLTLQPVGSSTISLRMGTNKITSQKGMSV<VKLGQQVYDLKYCAAPTEPVIHNGSQGTGTKGLEI

Parental  SDSDYQAEYPEEYRGEYQDDYPREYQYGDQGID
          S..DYQAEY..E..G.Y.D.YP...QYGDQG.D
Retrocopy SGNDYQAEYADE*HGTYHDAYPKDDQYGDQGTD

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_190 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_190 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.

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190 , retro_vpac_449,