RetrogeneDB ID: retro_ocun_566

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:72821432..72821919(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED5
• Ensembl ID: ENSOCUG00000012427
• Aliases: None
• Description: transmembrane emp24 protein transport domain containing 5 [Source:HGNC Symbol;Acc:24251]

Sequence

>retro_ocun_566
GTCCTGCCAGGGGTGGCAGGCTTTACTCCATCCTTAGACTGTGACTTCATCTTTACCCTTCCAACTGACCAGAAGGAGTG
TTTCTACCAGCCTATACTGCTAAGGGCCTCGCCAGAGATCAAGTACCAAGTTTTAGATGAAGTACTACAAGATACCTATT
TTCATCTTGCCTCTCCAGAAGGCAAAACCTTAGTTTTTGAACAAAGAAAATCAGATGCAGTTCACACTGTAGAGATGGAA
GATGGTGACTACATGGTTCTACTTTGACAATACATTTAGCACTACTTCTGAGAAGGTGGTTTTCTTTGAATTAATCCTTG
ATAATATGGGAGAACAGGCACAAGAACAAGAAGATTGGAAGAAATATATTATCAGCACAGAAATGCTAGGCATGAAACTG
GAAGATACCCAGGAATCCACTAATAGCATCAAGTCCAGACTAAGCAAAAGTGACCATATTCAAACTCTGCTGAGAGCATT
TGAAGCT

Alignment

ORF - retro_ocun_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.98 %
• Parental protein coverage: 70.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLPGAAGFTPSLDSDFTFTLPAGQKECFYQPMPLKASLEIEYQVLDGAGLDIDFHLASPEGKTLVFEQRK
          .LPG.AGFTPSLD.DF.FTLP..QKECFYQP..L.AS.EI.YQVLD....D..FHLASPEGKTLVFEQRK
Retrocopy VLPGVAGFTPSLDCDFIFTLPTDQKECFYQPILLRASPEIKYQVLDEVLQDTYFHLASPEGKTLVFEQRK

Parental  SDGVHTVETEDGDYM-FCFDNTFSTISEKVIFFELILDNMGEQAQEQEDWKKYITGTDMLDMKLEDILES
          SD.VHTVE.EDGDYM.F.FDNTFST.SEKV.FFELILDNMGEQAQEQEDWKKYI..T.ML.MKLED..ES
Retrocopy SDAVHTVEMEDGDYM>FYFDNTFSTTSEKVVFFELILDNMGEQAQEQEDWKKYIISTEMLGMKLEDTQES

Parental  INSIKSRLSKSGHIQTLLRAFEA
          .NSIKSRLSKS.HIQTLLRAFEA
Retrocopy TNSIKSRLSKSDHIQTLLRAFEA

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	0.00 RPM	10.98 RPM
SRP017611_kidney	0.00 RPM	19.06 RPM
SRP017611_liver	0.00 RPM	19.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_566 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012192	1 retrocopy	retro_cpor_254,
Oryctolagus cuniculus	ENSOCUG00000003453	1 retrocopy	retro_ocun_576,
Oryctolagus cuniculus	ENSOCUG00000012427	1 retrocopy	retro_ocun_566 ,
Rattus norvegicus	ENSRNOG00000000073	1 retrocopy	retro_rnor_620,
Ictidomys tridecemlineatus	ENSSTOG00000028196	1 retrocopy	retro_itri_155,