RetrogeneDB ID: retro_pcap_340

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_42243:13921..14563(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOSIP
• Ensembl ID: ENSPCAG00000016030
• Aliases: None
• Description: nitric oxide synthase interacting protein [Source:HGNC Symbol;Acc:17946]

Sequence

>retro_pcap_340
GGTTATGGGACACAAAACATTCGACTGAGCCGGGATGCGGTGAAGGACTTTGACTGCTGCTGTCTCTCTCTACGGCCCTG
CCATGACCCCGTTGTCACCCCAGACGGCTACCTATGTGAGCGTGAGGCCACCCTGGAGTACATTCTTCACCAGAAGAAGA
TTGCCCGACAGATGAAAGCATATGAGAAGCAGCGGGGTGCCCAGTCAGAGGAGCAGAAACAGCTGGAGCAGGCAGCTGCA
CAGGAACAGGTACGTGGCTTCCTGGAGAAGGAGGTGGCCACTGTTAGTCGGCCCCTCAACCCCTTCATGCCCAAGGCCGC
TTCTGAGAATGGCCCAGATGACGCCCGGCCGGGACTCAGTGCGAGCCACGCAAACAAGGACAAGGTGCTGCCCAGCTTCT
GGATCCCATCGCTGACGCTTGAGGCTAAAGCCACCAAGCTGGAGAAACTGTGTCGCAAGGTGACTTGCCCCATGTTGGGG
AAGCTGCTGCGTATGTCAGACCTGACGCCTGTGTGCTTCACGCTGCTCTACAGCTCCGTGGACCGCATGGGGCTGATCAC
GCGCAGCGAGCGCTATGTGTGTGCAGTGACCCACAACAGCTTAAGCAACGCCACGCCCGGCACGGGCTCCGGCCCTCTGG
GC

Alignment

ORF - retro_pcap_340 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 77.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYGTQNIRLSRD-VKD-DCCCLSLHP-HDPV-TPDGYLYEREAILEYILHQKKEIARQMKAYEKQRGARR
          GYGTQNIRLSRD.VKD.DCCCLSL.P.HDPV.TPDGYL.EREA.LEYILHQKK.IARQMKAYEKQRGA..
Retrocopy GYGTQNIRLSRDAVKDFDCCCLSLRPCHDPVVTPDGYLCEREATLEYILHQKK-IARQMKAYEKQRGAQS

Parental  EEQKELQRAAAQDQVRGFLEKEAAIVSRPLNPFTPKAPHENGSDDAQPGPSVP--GKDKVLPSFWIPSLT
          EEQK.L..AAAQ.QVRGFLEKE.A.VSRPLNPF.PKA..ENG.DDA.PG.S.....KDKVLPSFWIPSLT
Retrocopy EEQKQLEQAAAQEQVRGFLEKEVATVSRPLNPFMPKAASENGPDDARPGLSASHANKDKVLPSFWIPSLT

Parental  PEAKATKLEKPSRTVTCPMSGKPLRMSDLTPVRFTLLDSSVDRVGLITRSERYVCAVTRDSLSNATPCAV
          .EAKATKLEK..R.VTCPM.GK.LRMSDLTPV.FTLL.SSVDR.GLITRSERYVCAVT..SLSNATP...
Retrocopy LEAKATKLEKLCRKVTCPMLGKLLRMSDLTPVCFTLLYSSVDRMGLITRSERYVCAVTHNSLSNATPGTG

Parental  LRPSG
          ..P.G
Retrocopy SGPLG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_340 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000010497	2 retrocopies	retro_fcat_1424, retro_fcat_1471,
Macropus eugenii	ENSMEUG00000010446	1 retrocopy	retro_meug_837,
Myotis lucifugus	ENSMLUG00000017657	1 retrocopy	retro_mluc_2232,
Procavia capensis	ENSPCAG00000016030	1 retrocopy	retro_pcap_340 ,