RetrogeneDB ID: retro_vpac_172

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2338:367849..368334(+)
• Located in intron of: ENSVPAG00000006478

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRISP2
• Ensembl ID: ENSVPAG00000009962
• Aliases: None
• Description: cysteine-rich secretory protein 2 [Source:HGNC Symbol;Acc:12024]

Sequence

>retro_vpac_172
GATCCATCCTTTTCTACTTCGTTAGCTACTCAAACGGAAGTCCAAAGAGAGATTGTAAATAAACACAATGAGCTAAGGAA
ATCCGTCTCTCCACCTGTCAGCAACATACTAAAGATGGAATGGAGCAGAGACGCCACAGCAAATGCCCAGAAGGGGCAAA
CCAGTGTGCTATAGAACACAGTAATCCAGATGACCGATAGACCAGTACAAAATGTGGTGAGAATTTCTACATGTCAGGTG
ACTCTACTGCCTGGTCAGATGCGACCCAAAGCTGGTATGAAGAATGCCACGATTTTGTCTGTGGTGCAGAACTGAAGAGT
TCCGGTGCAGTCATTAGATATTATACCCAGCCTGTCTGGTACTCACCCTACCTTGCTGGATGTGGAATTGCTTGTTGTCC
TAATCAAGACAGTCTTAAATACTACTATGTTTGCCAATATTGTCCTGCTGGCAATAAAGTGAGTAAAAAGAATACAACTT
ACCAG

Alignment

ORF - retro_vpac_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.01 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPSFTALLTTQTEVQREIVNKHNELRKSVSPPARNMLKMEWSRDATANAQKW-ANKCTLEHSNPDDRKTS
          DPSF...L.TQTEVQREIVNKHNELRKSVSPP..N.LKMEWSRDATANAQK..AN.C..EHSNPDDR.TS
Retrocopy DPSFSTSLATQTEVQREIVNKHNELRKSVSPPVSNILKMEWSRDATANAQKG<ANQCAIEHSNPDDR*TS

Parental  TKCGENLYMSSDPVAWSDAIQSWYEERHNFVYGVGQKSPSAVIGHYTQLVWYSSYLVGCGIAYCPNQESL
          TKCGEN.YMS.D..AWSDA.QSWYEE.H.FV.G...KS..AVI..YTQ.VWYS.YL.GCGIA.CPNQ.SL
Retrocopy TKCGENFYMSGDSTAWSDATQSWYEECHDFVCGAELKSSGAVIRYYTQPVWYSPYLAGCGIACCPNQDSL

Parental  KYYYVCQYCPAMKAYFREGIHFQ
          KYYYVCQYCPA...........Q
Retrocopy KYYYVCQYCPAGNKVSKKNTTYQ

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_172 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_172 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000010302	1 retrocopy	retro_mluc_2168,
Monodelphis domestica	ENSMODG00000025686	1 retrocopy	retro_mdom_1586,
Vicugna pacos	ENSVPAG00000009962	1 retrocopy	retro_vpac_172 ,