RetrogeneDB ID: retro_ocun_439

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:11476705..11477893(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GZF1
• Ensembl ID: ENSOCUG00000025214
• Aliases: None
• Description: GDNF-inducible zinc finger protein 1 [Source:HGNC Symbol;Acc:15808]

Sequence

>retro_ocun_439
AACCTGAAGTGCGGCATCTGTGAGAAGGCCTTCTTGTACGAGAAGAGCTTCCTGAAGCACATCCGGCGGCACCACGGCGT
GGCCAGCGAGGTGGTGTACCGCTGTGACACCTGCGGCCAGACCTTCGCCAACCGCTGCAACCTGCGCAGCCACCAGCGCC
ACGTGCACAGCAGCGAGCGGCGCTTCCCCTGCGAGCTGTGCGGCAAGAAGTTCAAGCGCTAGAAGGACGTGAAGCGGCAC
GCAGTACAGGTGCACGAGGGCGGCGGCGAGCGGCACCGCTGCGGCCAGTGCGGCAAGGGCCTGAGCTCCAAGACGGCGCT
GCGGCTGCATGAGCGCACGCACACCGGCGACAGGCCCTAAGGCTGCACCGAGTGCGGGGCGAAGTTCTCGCAGCCGTCAG
CGCTCAAGACCCACATGAGAATCCACACCGGGGAAAAACCTTTCGTCTGTGATGAGTGTGGCGCAAGATTCACCCAGAAC
CACATGCTGATTTATCACAAAAGGTGCCACACAGGTGAGAGGCCTTTCATGTGTGAGACATGCGGCAAGAGTTTTGCTTC
GAAGGAGTACTTGAAACATCACAACAGAATCCACACTGGCTCGAAACCCTTTAAATGTGAAGTGTGCTTCCGGACTTTTG
CTCAGCGGAACTCCCTGTACCAGCACATCAAGGTCCACACAGGGGAGCGCCCCTACTGTTGTGACCAGTGTAGGAAGCAG
TTCACCCAGCTCAACGCCTTACAGCGCCACCATCGGATCCACAGGGGCGAGAAGCCGTTAATGTGCAACGCTTGCGGGCG
CACGTTCACGGACAAGTCCACTCTGCGGCGGCACACCTCTATACACGATAAGAATACTCCATGGAAGTCTTTCCTTGTCA
TTGTAGATGGCTCCCCCAAGAACGACGAGGGTCACAAGACAGAACAGCCGGATGAAGAGTACGTGCCGCCCAAGCTTTCA
GATAAACTGCTGTCTTTTGCAGAAAGCAGCCACTTTCACGGCCTGGCCGCGGTGCCCGGCAGTGTCGCCCCCGCCCACGA
CGGCAATGCCGCAGACACCGCCTGCAAGGCCGACGCCGCCGTGGTGTCCCAGGACGCCCTGCTGGCCACCACCCTCAGTG
AGCTCAGCGAGCTGAGCCCGCAGGCGGACGCGATGCCCGCCCAGCTGCACCCCTTGACCAGCATGGAG

Alignment

ORF - retro_ocun_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 57.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLKCGVCEKAFLYEKSFLKHIRRHHGVASEVVYRCDTCGQTFANRCNLRSHQRHVHSSERRFPCELCGKK
          NLKCG.CEKAFLYEKSFLKHIRRHHGVASEVVYRCDTCGQTFANRCNLRSHQRHVHSSERRFPCELCGKK
Retrocopy NLKCGICEKAFLYEKSFLKHIRRHHGVASEVVYRCDTCGQTFANRCNLRSHQRHVHSSERRFPCELCGKK

Parental  FKRKKDVKRHVVQVHEGGGERHRCGQCGKGLSSKTALRLHERTHTGDRPYGCTECGAKFSQPSALKTHMR
          FKR.KDVKRH.VQVHEGGGERHRCGQCGKGLSSKTALRLHERTHTGDRP.GCTECGAKFSQPSALKTHMR
Retrocopy FKR*KDVKRHAVQVHEGGGERHRCGQCGKGLSSKTALRLHERTHTGDRP*GCTECGAKFSQPSALKTHMR

Parental  IHTGEKPFVCDECGARFTQNHMLIYHKRCHTGERPFMCETCGKSFASKEYLKHHNRIHTGSKPFKCEVCF
          IHTGEKPFVCDECGARFTQNHMLIYHKRCHTGERPFMCETCGKSFASKEYLKHHNRIHTGSKPFKCEVCF
Retrocopy IHTGEKPFVCDECGARFTQNHMLIYHKRCHTGERPFMCETCGKSFASKEYLKHHNRIHTGSKPFKCEVCF

Parental  RTFAQRNSLYQHIKVHTGERPYCCDQCGKQFTQLNALQRHHRIHTGEKPFMCNACGRTFTDKSTLRRHTS
          RTFAQRNSLYQHIKVHTGERPYCCDQC.KQFTQLNALQRHHRIH.GEKP.MCNACGRTFTDKSTLRRHTS
Retrocopy RTFAQRNSLYQHIKVHTGERPYCCDQCRKQFTQLNALQRHHRIHRGEKPLMCNACGRTFTDKSTLRRHTS

Parental  IHDKNTPWKSFLVIVDGSPKNDEGHKTEQPDEEYVPPKLSDKLLSFAESSHFHGLAAVPGNVAPAHDGNA
          IHDKNTPWKSFLVIVDGSPKNDEGHKTEQPDEEYVPPKLSDKLLSFAESSHFHGLAAVPG.VAPAHDGNA
Retrocopy IHDKNTPWKSFLVIVDGSPKNDEGHKTEQPDEEYVPPKLSDKLLSFAESSHFHGLAAVPGSVAPAHDGNA

Parental  ADTACKADAAVVSQDALLATTLSELSELSPQADAMPAQLHPLTSME
          ADTACKADAAVVSQDALLATTLSELSELSPQADAMPAQLHPLTSME
Retrocopy ADTACKADAAVVSQDALLATTLSELSELSPQADAMPAQLHPLTSME

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	0.94 RPM	4.47 RPM
SRP017611_kidney	0.30 RPM	4.26 RPM
SRP017611_liver	0.46 RPM	3.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_439 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000025214	1 retrocopy	retro_ocun_439 ,