RetrogeneDB ID: retro_vpac_650

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_95759:535..1353(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000000617
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KCMF1
• Ensembl ID: ENSVPAG00000010386
• Aliases: None
• Description: potassium channel modulatory factor 1 [Source:HGNC Symbol;Acc:20589]

Sequence

>retro_vpac_650
ATTTGCCCGATATGCGCGGCCTTGCCTGGAAGCGACCCCAAACACGTCACGGACGACTTCGCAGCCCATCTCACACTTGA
ACACCGGGCCCCTAGAGATTTATATGAATTGATTGGTGTTCGACACGTACGTAGAATGTCCCACCCCGGCCGGGGCTTAG
GAGGGCCCCGAGCTCGCAGGTCAAACATGTACTTTACCAGCAGCTCTGCTCGCGGCCTCTCTTCCTCTCAGAGCTCGTAT
TCTCCAAGCAGCCCGGAAGCCATGGATCCTATAGCTGAGCTTTTACCTCAGTTGTCAGGCGTGAGACGTTCTGCAGGAGG
ACAGCTTAACTCTTCTGGCCCTTCCGCTTCTCAGTTACAGCAGCTGCAGATGCAGCTGCAGCTGGAACGGCAGCACGCCC
AGGCCGCGCGCCAGCAGCTGGAGACCGCGCTCAACGCCTCCCTGCGCTCCAACGCCAGCAGCGTCACCACTGCGGTCACG
CAGTCCACGGCGACGGCCAGCACAGCCAACACGGAAAGCAGTCAGCAGGCGCTGCAGAACTCCCAGTTTCTTTTAACAAG
GTTGATGACCCTAAGCTGTCCGAAGCAGAGCGCCAGTGCATGGAGAGCGAGCGCGCGGACCGCAGCCTGTTCGTGCAGGA
GCTGCTCCTGTCCACGCTGGTGCGCGAGGAGAGCTCGTCCTCGGACGAGGAGGAACGGGGGGAGATGGCAGATTTCGGTG
CTATGGGCTGTGTAGATATTATGCCTTTAGATGTCGCTTTAGAAAACCTAAATCTGAAAGAGAGTAATAAAGGAAATGAG
CCTCCACCACCTCCTCTT

Alignment

ORF - retro_vpac_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ICPICAALPGGDPNHVTDDFAAHLTLEHRAPRDLDESSGVRHVRRMFHPGRGLGGPRARRSNMHFTSSSA
          ICPICAALPG.DP.HVTDDFAAHLTLEHRAPRDL.E..GVRHVRRM.HPGRGLGGPRARRSNM.FTSSSA
Retrocopy ICPICAALPGSDPKHVTDDFAAHLTLEHRAPRDLYELIGVRHVRRMSHPGRGLGGPRARRSNMYFTSSSA

Parental  GGLSSSQSSYSPSXXXXXXXXXXELLSQLSGVRRSAGGQLNSSGPSASQLQQLQMQLQLERQHAQAARQQ
          .GL.SS..S..............ELL.QLSGVRRSAGGQLNSSGPSASQL.........ERQHAQAARQQ
Retrocopy RGL-SSSQSSYSPSSPEAMDPIAELLPQLSGVRRSAGGQLNSSGPSASQLXXXXXXXXXERQHAQAARQQ

Parental  LETARNATRRSNASSVTAAVTQSTATASTANTDSSQQALQNSQFLLTRL-NDLKLSEAEPQCMESE-PDR
          LETA.NA..RSNASSVT.AVTQSTATASTANT.SSQQALQNSQFLLTRL..D.KLSEAE.QCMESE..DR
Retrocopy LETALNASLRSNASSVTTAVTQSTATASTANTESSQQALQNSQFLLTRL<DDPKLSEAERQCMESERADR

Parental  SLFVQELLLSTLVREESSSSDEEEPGEMADFGAMGCVDIMPLDVALENLNLKESNKGNEPPPPPL
          SLFVQELLLSTLVREESSSSDEEE.GEMADFGAMGCVDIMPLDVALENLNLKESNKGNEPPPPPL
Retrocopy SLFVQELLLSTLVREESSSSDEEERGEMADFGAMGCVDIMPLDVALENLNLKESNKGNEPPPPPL

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_650 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_650 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005786	1 retrocopy	retro_chof_1282,
Dasypus novemcinctus	ENSDNOG00000006752	2 retrocopies	retro_dnov_1000, retro_dnov_2063,
Echinops telfairi	ENSETEG00000001809	1 retrocopy	retro_etel_1685,
Myotis lucifugus	ENSMLUG00000000979	1 retrocopy	retro_mluc_1781,
Monodelphis domestica	ENSMODG00000015567	1 retrocopy	retro_mdom_1682,
Otolemur garnettii	ENSOGAG00000034863	2 retrocopies	retro_ogar_3140, retro_ogar_397,
Vicugna pacos	ENSVPAG00000010386	1 retrocopy	retro_vpac_650 ,