RetrogeneDB ID: retro_vpac_97

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1792:52838..53306(-)
• Located in intron of: ENSVPAG00000002905

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSVPAG00000004374
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa) [Source:HGNC Symbol;Acc:5036]

Sequence

>retro_vpac_97
TATTTGTCTTGATTTGGGGAAGTTGTAGACTGCACAGTTAAAACAGATCTTGTCACTGGAAGATCAAGAGGATTTGGATT
TGTGCTTTTCAAAGATGCTGCTAGTGTTAATAAGGTTTTGGAACTGAAAGAACACAAACTGGATAGCAAATTGACAGACC
CTGAAAGGGCCAAAGCTTTAAAAGGGAAGGAACCCCCAAAAATATTTTTTGGGTGAATTGAGCCCAGATACTTCTGAAGA
ACAAATTAAAGAATGTTTTGGAGCCTTTGGAGAGATTGAAAACATAGAACTTCCCATGGATACAAAAACAAATGAAAGAA
GAGGATTTTGTTTACATATACAGATGAAGAGCCAGTAAAGAAACTGTTAGAAAGCAGATTTCATCAAATTGGTTCTGGAA
AGTGTGAAGTTAAACTTGCTCAGCCCAAAGAGGTATATAGGCAGCAACAGCAACAAAAAAAGGAGGGA

Alignment

ORF - retro_vpac_97 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.12 %
• Parental protein coverage: 61.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPVKKIF
          Y.S.FGEVVDCT.K.D..TGRSRGFGFVLFK...SV.KV...KEHKL..K..DP.RAKA.K.KEP..KIF
Retrocopy YLS*FGEVVDCTVKTDLVTGRSRGFGFVLFKDAASVNKVLELKEHKLDSKLTDPERAKALKGKEP-PKIF

Parental  -VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFC-FITFKEEEPVKKIMEKKYHNVGLSKCE
          ..G.LSPDT.EE.I.E.FG.FGE.E.IELPMD.KTN.RRGFC.F....EE.PVKK..E...H..G..KCE
Retrocopy >LGELSPDTSEEQIKECFGAFGEIENIELPMDTKTNERRGFC<FTYTDEE-PVKKLLESRFHQIGSGKCE

Parental  IKVAMSKEQYQQQQQWGSRG
          .K.A..KE.Y.QQQQ....G
Retrocopy VKLAQPKEVYRQQQQQKKEG

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_97 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_97 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97 ,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,