RetrogeneDB ID: retro_vpac_651

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_965:309363..310012(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000010621
• Aliases: None
• Description: None

Sequence

>retro_vpac_651
AGGGCCCTGCTGTCCCTGTAGCCTCTGGCCACACCACTGGTGTTGTCATGGATCCTGGGGAGGGGGTTGCCCACAGGTGC
CCATCTATGAGGGGTACGTCCTCCTCCATGCCATCCTGCGTCTGCACCTGGCTGTCCTGGGACCTGACTGGCTGCCTCGT
GAAGGTGCTCATGGGGTGTGGCTGCATCCTCCGCACCACGGCCCCGTGGGAAATTGTGCATGACATCAAGGGCAGCTGTG
CTATGTCACCCTGGACACGGGGCAGGAGATGGTCACTGCGGTGCCCGCCTCCTCCCTGGAGAAGAGCTCTGAGCTCTCTG
ACCATCAGTGGTCACCATCCTCAACGAGTGTTTCTGGGTCCAGAGGCGCTCTTCCACCCTCCTCCTGGGCATGGAGTCCC
ATGGCACCCCCGAGACCACCTTCACCTCCATGCTGAAGGGTGATGTCGATAGCCGGAAGGCCTGTGTGCCAACACAGTGC
TGTCTGGGCGGGACCACCGTGTACCTCGCATCACCACCAGGATGTACGGGGATCTCAGGACACTGGCCCCCACACGACTG
AAGATCAGATCAAGACCAAGGCTCCTCCTGAACACAAGTACTGGGTGTGGGTCTGGGGGGCCATCCTGGCCTCGCTGTCT
GCCTTCCAG

Alignment

ORF - retro_vpac_651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.71 %
• Parental protein coverage: 64.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 12

Retrocopy - Parental Gene Alignment:

Parental  QAVLSL-YASGRTTGIVLDSGDGVTHN-VPIYEGYALPHAIMRLDLA-GRDLTDYLMKILTERGYSFVTT
          .A.LSL..ASG.TTG.V.D.G.GV.H..VPIYEGY.L.HAI.RL.LA...DLT..L.K.L...G....TT
Retrocopy RALLSL<VASGHTTGVVMDPGEGVAHR<VPIYEGYVLLHAILRLHLA>SWDLTGCLVKVLMGCGCILRTT

Parental  AEREIVRDIKE-KLCYVALDFENEMATAASSSSLEKSYELPDGQ-VITIGNERFRC-PETLFQ-PS-FIG
          A..EIV.DIK...LCYV.LD...EM.TA...SSLEKS.EL.D.Q.V.TI.NE.F...PE.LF..PS...G
Retrocopy APWEIVHDIKG<QLCYVTLDTGQEMVTAVPASSLEKSSELSDHQ<VVTILNECFWV<PEALFH<PS<LLG

Parental  MESAGIHETTYNSIMKCDIDIRK-DLYANNVLSG-GTTMY-PGIADRMQKEITALA-PSTMK--IKIIAP
          MES.G..ETT..S..K.D.D.RK..L.AN.VLSG.GTT.Y.P.I..RM......LA.P.T....IK..AP
Retrocopy MESHGTPETTFTSMLKGDVDSRK<GLCANTVLSG>GTTVY<PRITTRMYGDLRTLA<PHTTEDQIKTKAP

Parental  PERKYSVWIGGSILASLSTFQ
          PE.KY.VW..G.ILASLS.FQ
Retrocopy PEHKYWVWVWGAILASLSAFQ

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_651 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_651 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 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000005463	1 retrocopy	retro_meug_970,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651 ,