RetrogeneDB ID: retro_ocun_1414

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:53632931..53633496(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021190
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YEATS4
• Ensembl ID: ENSOCUG00000011552
• Aliases: None
• Description: YEATS domain containing 4 [Source:HGNC Symbol;Acc:24859]

Sequence

>retro_ocun_1414
GAAGAAGATGGGCACACACATCGGTGGACGGTGTATGTAAAGCCATATAGAAATGAGGATATGTCGGCATATGTGAAGAA
AATCCAATTTAAATTGCACGAAAGCTATGGCAATCCTTTAAGAGTTGTTACTAAGCCTCCATATAAAATTACTGAAACAG
GATGGGTGAATTTAAATAATCAACAAGATATTTTTTATTGCCCCTAATGAAAGACCTGTAACCCTGTATCGTTTATTAAA
ACTATTTCAATCAGACACGGATGCAATGCTGGGAAAAAAGACAGTGGTTTCAGAGTTCTGTGATGAAATGATATTTCAAG
ATCCAACAGCAACGATGCAACAATTATTAACAACATCGCGTCAGCTAACATTAGGAGCCTATAAGCATGAAACAGAATTT
GCAGAACTTGAAGTGAAAACTAGAGAAAAATTAGAAGCTGCCAAGAAAAAAACAAGCTTTGAAATTGCAGAGCTGAAGGA
GAGATTAAAAGCAAATCGTGAAACTATAAATTGTTTAAAAAATGAAATCAGGAAACTTGAGGAAGATGATCAGACAAAAG
ACATA

Alignment

ORF - retro_ocun_1414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.72 %
• Parental protein coverage: 83.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEDGHTHQWTVYVKPYRNEDMSAYVKKIQFKLHESYGNPLRVVTKPPYEITETGW-GEFE-IIIKIFFID
          EEDGHTH.WTVYVKPYRNEDMSAYVKKIQFKLHESYGNPLRVVTKPPY.ITETGW.GEF..II.KIFFI.
Retrocopy EEDGHTHRWTVYVKPYRNEDMSAYVKKIQFKLHESYGNPLRVVTKPPYKITETGW<GEFK<IINKIFFIA

Parental  PNERPVTLYHLLKLFQSDTNAMLGKKTVVSEFYDEMIFQDPTAMMQQLLTTSRQLTLGAYKHETEFAELE
          PNERPVTLY.LLKLFQSDT.AMLGKKTVVSEF.DEMIFQDPTA.MQQLLTTSRQLTLGAYKHETEFAELE
Retrocopy PNERPVTLYRLLKLFQSDTDAMLGKKTVVSEFCDEMIFQDPTATMQQLLTTSRQLTLGAYKHETEFAELE

Parental  VKTREKLEAAKKKTSFEIAELKERLKASRETINCLKNEIRKLEEDDQTKDI
          VKTREKLEAAKKKTSFEIAELKERLKA.RETINCLKNEIRKLEEDDQTKDI
Retrocopy VKTREKLEAAKKKTSFEIAELKERLKANRETINCLKNEIRKLEEDDQTKDI

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	0.06 RPM	12.86 RPM
SRP017611_kidney	0.00 RPM	15.41 RPM
SRP017611_liver	0.00 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1414 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010793	1 retrocopy	retro_etel_836,
Microcebus murinus	ENSMICG00000002467	1 retrocopy	retro_mmur_1433,
Monodelphis domestica	ENSMODG00000020377	1 retrocopy	retro_mdom_1545,
Nomascus leucogenys	ENSNLEG00000003837	1 retrocopy	retro_nleu_816,
Oryctolagus cuniculus	ENSOCUG00000011552	1 retrocopy	retro_ocun_1414 ,
Tursiops truncatus	ENSTTRG00000013951	2 retrocopies	retro_ttru_226, retro_ttru_295,