RetrogeneDB ID: retro_ocun_440

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:12741016..12741975(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHN2
• Ensembl ID: ENSOCUG00000009401
• Aliases: None
• Description: chimerin 2 [Source:HGNC Symbol;Acc:1944]

Sequence

>retro_ocun_440
ACAACAGACCCCATCTATGAGCACATGGGCTATGCCACTCTGCTCTGAGAATAAGTCTCCAGGAGGCTGAGCAGGTCCAA
AAACGAGTCCAGGAAAATGAGTGTCACAAGTGAAGAGCACCAGGCGTGGAGAAGATCTCCTGCCTGGTCCGAAGGACCGC
CCTCACACACAACGACAACCACTTCAACTATGAGAAGACACACAACTTTAAGGTGCACACTTTCCGAGGCCCACACTGGT
GTGAATACTGTGCCAACTTCATGTGGGGGCTCATTGCCCAGGGGGTCCGGTGCTCAGGCTGTGGGCTGAATGTGCACAAG
CAGTGCTCCAAGCAGGTGCCCAACGACTGCCAGCCCGACCTCAAGAGGATCAAGAAGGTGTACTGTTGTGACCTGACCAC
GCTCGTGAAGGCCCACAACACGCAGAGACCCATGGTGGTGGACATGTGCATCCGGAGATTGAAGCGAGAGGATTAACATC
AGAAGGAAGTTACAGTCTCCGGGTTCACTGAGCACATCAAGGATGTCAAGATGGCATTTGACAGAGATGGAGAAAAGGCA
GACATATCTGCCAACATCTACCCAGACATCAACATCATCACTGGAGCCCTGAAATTCTACTTCCGAGACCTGCCCATCCC
TGTCATCACATAAGGCACCTATTCCAAATTCATAGAGACAGCAAAATTCTCCAGTGCAGATGAGAGGCTGGAAGCCGTCC
ACGAAGTGCTGATGCTGCTGCCGCCTGCCCACTACGAGACCCTGCGCTACCTGATGAGCCACCTCAAGAAGGTCACCCTG
AACGAGAAGGACAATTTCGTGAACGCGGAAAACCTGGGGATCGTGTTCGGGCCCACGCTGATGAGGCCGCCCGAGGACAA
CACCCTCACCACCCTGCACAACATGCAGTACCAGAAGCTGATTGTGCAGATTTTGATAGAAAACGAAGATGTTCTGTTC

Alignment

ORF - retro_ocun_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 85.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTNPIYEHIGYATLLREKVSRRLSRSKNESRKTSVTSEEH-PGVEKISSLVRRAALTHNDNHFNYEKTHN
          TT.PIYEH.GYATLL.E.VSRRLSRSKNESRK.SVTSEEH.PGVEKIS.LVRR.ALTHNDNHFNYEKTHN
Retrocopy TTDPIYEHMGYATLL*E*VSRRLSRSKNESRKMSVTSEEH<PGVEKISCLVRRTALTHNDNHFNYEKTHN

Parental  FKVHTFRGPHWCEYCANFMWGLIAQGVRCSDCGLNVHKQCSKHVPNDCQPDLKRIKKVYCCDLTTLVKAH
          FKVHTFRGPHWCEYCANFMWGLIAQGVRCS.CGLNVHKQCSK.VPNDCQPDLKRIKKVYCCDLTTLVKAH
Retrocopy FKVHTFRGPHWCEYCANFMWGLIAQGVRCSGCGLNVHKQCSKQVPNDCQPDLKRIKKVYCCDLTTLVKAH

Parental  NMQRPMVVDMCIREIEARGLKSEGIYRVSGFTEHIEDVKMAFDRDGEKADISANIYPDINIITGALKLYF
          N.QRPMVVDMCIR..............VSGFTEHI.DVKMAFDRDGEKADISANIYPDINIITGALK.YF
Retrocopy NTQRPMVVDMCIRRLKRED*HQKEV-TVSGFTEHIKDVKMAFDRDGEKADISANIYPDINIITGALKFYF

Parental  RDLPIPVITYDTYSKFIEAAKVSSADERLEAVHEVLMLLPPAHYETLRYLMIHLKKVTLNEKDNFMNAEN
          RDLPIPVIT..TYSKFIE.AK.SSADERLEAVHEVLMLLPPAHYETLRYLM.HLKKVTLNEKDNF.NAEN
Retrocopy RDLPIPVIT*GTYSKFIETAKFSSADERLEAVHEVLMLLPPAHYETLRYLMSHLKKVTLNEKDNFVNAEN

Parental  LGIVFGPTLMRPPEDNTLTTLHDMRYQKLIVQILIENEDVLF
          LGIVFGPTLMRPPEDNTLTTLH.M.YQKLIVQILIENEDVLF
Retrocopy LGIVFGPTLMRPPEDNTLTTLHNMQYQKLIVQILIENEDVLF

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	0.11 RPM	47.08 RPM
SRP017611_kidney	0.00 RPM	3.65 RPM
SRP017611_liver	0.00 RPM	6.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_440 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003023	1 retrocopy	retro_cfam_2185,
Macaca mulatta	ENSMMUG00000008329	1 retrocopy	retro_mmul_1926,
Oryctolagus cuniculus	ENSOCUG00000009401	1 retrocopy	retro_ocun_440 ,
Sus scrofa	ENSSSCG00000016687	1 retrocopy	retro_sscr_939,