RetrogeneDB ID: retro_ocun_654

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:75477010..75477348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSOCUG00000024282
• Aliases: None
• Description: pleckstrin homology domain containing, family B (evectins) member 2 [Source:HGNC Symbol;Acc:19236]

Sequence

>retro_ocun_654
GCAGAAAGCTCAGATGATTGGTTGGCCTGGAAATTTACACTGCAGGATTCTAGGACAAACACAGCTTACGTGGGCTCCTC
AATCCTGTCTGAAGAGAGAGCTGTGGCTTCCTCCCGACCTCCCTACACATCCTATGCTGTGGCAATCCCTGAGTAGGCTT
ATGGCTCCAGTACCTATAGGGGCACTTACCCAGTAGGAACTCAAGTTGTCTATGCTGCGAATGGGCAGGCATACGCTGTG
TGTACCCGTATGCTAGACATTACAGAGGGCAGCCCACCAACCAAGTCCTCATTCGTGAGTGGGATCGAGACAACGACAGT
GATCTGGTGCTGGGCATG

Alignment

ORF - retro_ocun_654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 51.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AESTDDCLAWKFTLQDSRTNTAYVGSAILSDETAVASSPPPYTAYAAPIPEQAYGYGPYSGAYPTGTQVV
          AES.DD.LAWKFTLQDSRTNTAYVGS.ILS.E.AVASS.PPYT.YA..IPE.AYG...Y.G.YP.GTQVV
Retrocopy AESSDDWLAWKFTLQDSRTNTAYVGSSILSEERAVASSRPPYTSYAVAIPE*AYGSSTYRGTYPVGTQVV

Parental  YAANGQAYAV-PYQYPYAGLYGQQPTNQVIIRERYRDNDSDLALGM
          YAANGQAYAV..Y.Y..A..Y..QPTNQV.IRE..RDNDSDL.LGM
Retrocopy YAANGQAYAV<VYPY--ARHYRGQPTNQVLIREWDRDNDSDLVLGM

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	168.05 RPM
SRP017611_kidney	0.00 RPM	87.98 RPM
SRP017611_liver	0.00 RPM	33.60 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_654 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654 ,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,