RetrogeneDB ID: retro_ocun_681

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:5779814..5780555(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027919
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIGK
• Ensembl ID: ENSOCUG00000005695
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class K [Source:HGNC Symbol;Acc:8965]

Sequence

>retro_ocun_681
GTATTCCTGACAGATGATATGGCATGCAACCCTAGAAACCCGAAACCAGCTACTGTGTTTAGTCACAAAAATATGGAGCT
AAATGTGTATGGAGATGATGTGGAAGTGGATTATAGAAGCTATGAGGTAACAGTGGAGAATTTTTTACGGGTATTAACTG
GGAGGATCCCACCTAGTACTCCTCGGTCAAAACGCCTTCTTTCTGATGATAGAAGCAATATTCTTATTTATATGACAGGA
CATGGTGGAAATGGTTTCTTGAAATTTCAAGATTCTGAAGAAATTACCAACATAGAACTTGCAGATGCTTTTGAACAAAT
GTGGCAGAAAAGACGCTACAATGAACTACTGTTTATTATTGACACTTGTCAAGGAGCATCCATGTATGAGCGATTTTATT
CTCCTAACATAATGGCTCTGGCTAGTAGTCAAGTGGGAGAAGATTCTCTCTCGCATCAACCTGATCCTGCAATTGGAGTT
CATCTTATGCATAGATACACATTTTATGTCTTGGAATTTTTGGAAGAAATTAATCCAGCTAGTCAAACTAATATGAATGA
CCTTTTCCAGGTATGTCCTAAAAGTCTGTGTGTATCTACTCCTGGACATCGCATTGATCTTTTCCAGAGGGATCCTAAAA
ATGTCCTGATAACTGATTTCTTTGGAAGTGTACGGAAAGTGGAGATTACAACAGAGACCATTAGTTTGCAACTGGATTCA
GAAATCATGGAGAGCAGCTTT

Alignment

ORF - retro_ocun_681 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.43 %
• Parental protein coverage: 74.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMLADDMACNPRNPKPATVFSHKNMELNVYGDDVEVDYRSYEVTVENFLRVLTGRIPPSTPRSKRLLSDD
          ..L.DDMACNPRNPKPATVFSHKNMELNVYGDDVEVDYRSYEVTVENFLRVLTGRIPPSTPRSKRLLSDD
Retrocopy VFLTDDMACNPRNPKPATVFSHKNMELNVYGDDVEVDYRSYEVTVENFLRVLTGRIPPSTPRSKRLLSDD

Parental  RSNILIYMTGHGGNGFLKFQDSEEITNIELADAFEQMWQKRRYNELLFIIDTCQGASMYERFYSPNIMAL
          RSNILIYMTGHGGNGFLKFQDSEEITNIELADAFEQMWQKRRYNELLFIIDTCQGASMYERFYSPNIMAL
Retrocopy RSNILIYMTGHGGNGFLKFQDSEEITNIELADAFEQMWQKRRYNELLFIIDTCQGASMYERFYSPNIMAL

Parental  ASSQVGEDSLSLCPSPSFCPHVGECLCIWSCLHMKNIKNYSKFGFNKRFQVCPKSLCVSTPGHRIDLFQR
          ASSQVGEDSLS..P.P....H...............I...S....N..FQVCPKSLCVSTPGHRIDLFQR
Retrocopy ASSQVGEDSLSHQPDPAIGVHLMHRYTFYVLEFLEEINPASQTNMNDLFQVCPKSLCVSTPGHRIDLFQR

Parental  DPKNVLITDFFGSVRKVEITTETISLQLDSEIMESRY
          DPKNVLITDFFGSVRKVEITTETISLQLDSEIMES..
Retrocopy DPKNVLITDFFGSVRKVEITTETISLQLDSEIMESSF

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	7.34 RPM	5.08 RPM
SRP017611_kidney	8.62 RPM	5.57 RPM
SRP017611_liver	1.62 RPM	1.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_681 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_681 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005695	1 retrocopy	retro_ocun_681 ,