RetrogeneDB ID: retro_ocun_1546

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02082490:9151..9802(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008766
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZFAND5
• Ensembl ID: ENSOCUG00000000795
• Aliases: None
• Description: zinc finger, AN1-type domain 5 [Source:HGNC Symbol;Acc:13008]

Sequence

>retro_ocun_1546
AAGCAGGAAAATATGGCTCAGGAGACTAACCAGACTCCAGGGCCTATGCTGTGTAGCACAGGATGTGGCTTTTATGGGAA
TCCTAGGACAAATGGAATGTGTTCTGTTTGCTACAAAGAGCATCTTCAGAGACAGCAGAATAGTGGCAGAATGAGCCCAA
TGGGGACAGCTAGTGGTTCCAACAGTCCTACCTCAGACTCTGCATCTGTACAAAGAGCAGACGCTAGCTTAAACAACTGT
GAAAGTGCTGCTGGTAGCACATCTGAAAAATCAAGAAATGTGCCTGTGGCTGCCTTGCCTGTAACTCAGCAAATGACAGA
AATGAGCATTTCAAGAGAGGACAAAATAACTACCCCGAAAACAGAGGTGTCAGAGCCAGTTGTCACTCAGCCCAGTCCAT
CAGTTTCTCAGCCCAGTACTTCTCAAAGTGAAGAAAAAGCTCCTGAGTTACCCAAACCAAAGAAGAACAGATGTTTCATG
TGTAGAAAGAAAGTTGGCCTTACAGGGTTTGACTGCCGATGTGGAAATTTGTTTTGTGGACTTCACCGTTATTCTGACAA
GCACAACTGTCCTTATGATTATAAAGCAAAAGCTGCAGCAAAAATCAGGAAAGAGAATCCAGTTGTTGTGGCTGAAAAAA
TCCAGAGAATA

Alignment

ORF - retro_ocun_1546 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.08 %
• Parental protein coverage: 81.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQENMAQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQQNSGRMSPMGTASGSNSPTSDSASV
          .QENMAQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQQNSGRMSPMGTASGSNSPTSDSASV
Retrocopy KQENMAQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQQNSGRMSPMGTASGSNSPTSDSASV

Parental  QRADASLNNCESAAGSTSEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVSQPST
          QRADASLNNCESAAGSTSEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVSQPST
Retrocopy QRADASLNNCESAAGSTSEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVSQPST

Parental  SQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKAEAAAKIRKENPVVV
          SQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKA.AAAKIRKENPVVV
Retrocopy SQSEEKAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKAKAAAKIRKENPVVV

Parental  AEKIQRI
          AEKIQRI
Retrocopy AEKIQRI

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	4.53 RPM	24.72 RPM
SRP017611_kidney	1.22 RPM	10.85 RPM
SRP017611_liver	1.70 RPM	8.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1546 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546 ,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23,