RetrogeneDB ID: retro_ocun_1683

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018762:209346..210397(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025527
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SYNCRIP
• Ensembl ID: ENSOCUG00000000601
• Aliases: None
• Description: synaptotagmin binding, cytoplasmic RNA interacting protein [Source:HGNC Symbol;Acc:16918]

Sequence

>retro_ocun_1683
AAAAAAGCAGCTCAGGAGGCTTTTAAACTGTATAATAATCATGAAATTCGTTCTGGAAAACATATTGGTGTCTGCATCTC
GGTTGCCAACAATAGGCTTTTTGTGGGCTCTATTCCTAAGAGTAAAACCAAGGAACAGCTTCTTGAAGAATTTAGCAAAG
TAACAGAGGGTCTTACAGACGTCATTTTATACCACCAACCAGATGACAAGAAAAAAAAAAAAACAGAGGCTTTTGCTTTC
TTGAATATGAAGATCATAAAACAGCTGCCCAGGCAAGGTGTAGGCTAATTAGTGGTAAAGTCAAGGTCTGGAAAAATGTT
GGAACTGTTGAATGGGCTGATCCTATAGAAGATCCTGATCCTGAGGTTATGGCAAAGGTGAAGGTACTTTTTGTATGTAA
CCTTGCCAATACTGTAACAGAAGAGATTTTAGAAAAGGCATTTAGTCAGTTTGGAAAACTGGAACGAATAAGGAAACTGA
AAGATTATGCATTCATTCATTTTGATGAACGAGATGGTGCAGTTAAGGCTATGGAAGAAATGAATGTCAAAGACTTGGAG
GGAGAAAACATTGAAATTGTTTTTGCTAAGCCACCAGATCAGAAAAGGAAAGAAAGAAAAGCTCAGAGGCAAGCAGCCAT
CAGATGTATGATGATTACTGCTATTATGGTCCAATTCATATGCCCCCTCCAACAAGAGGTAGAGGGCGTGGAGGTAGAGG
TGGTTATGGATATCCTCCAGATTATTATGGATATGAAGATTATTATGATTATTTTGGCTATGATTACCATAACTATCATG
GTGGATATGAAGATCCATACTATGGTTATGAAGATTTTCAAGTTGGAGCTAGAGGAAGGGGTGGTAGAGGAGTAAGGGGT
GCTGCTCCATCCAGAGGTCATGGGGCTGCTCCTCCCTGTGGTAGAGCCGGTTATTCACAGAAAGGAGGTCCTGGATCAGC
AAGAGGCATTGGTGGTGTGAGAGGAGGTGCCCAACAACAAAGAGGCCACGGGCAGGGAAAAGGGGTTGAGGCCTGTCCTG
ACCTGTTACAA

Alignment

ORF - retro_ocun_1683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.55 %
• Parental protein coverage: 62.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQPDDK
          K.AAQEA.KLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQ.LEEFSKVTEGLTDVILYHQPDDK
Retrocopy KKAAQEAFKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQLLEEFSKVTEGLTDVILYHQPDDK

Parental  KKNR--GFCF-LEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRNLANTV
          KK.....F.F.LEYEDHKTAAQAR.RL.SGKVKVW.NVGTVEWADPIEDPDPEVMAKVKVLFV.NLANTV
Retrocopy KKKKTEAFAF<LEYEDHKTAAQARCRLISGKVKVWKNVGTVEWADPIEDPDPEVMAKVKVLFVCNLANTV

Parental  TEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ
          TEEILEKAFSQFGKLER..KLKDYAFIHFDERDGAVKAMEEMN.KDLEGENIEIVFAKPPDQKRKERKAQ
Retrocopy TEEILEKAFSQFGKLERIRKLKDYAFIHFDERDGAVKAMEEMNVKDLEGENIEIVFAKPPDQKRKERKAQ

Parental  RQAAKNQMY-DDYYYYGPPHMPPPTRGRGRGGRGGYGYPPDYYGYEDYYDYYGYDYHNYRGGYEDPYYGY
          RQAA...M..D..YY.GP.HMPPPTRGRGRGGRGGYGYPPDYYGYEDYYDY.GYDYHNY.GGYEDPYYGY
Retrocopy RQAAIRCMM<DYCYY-GPIHMPPPTRGRGRGGRGGYGYPPDYYGYEDYYDYFGYDYHNYHGGYEDPYYGY

Parental  EDFQVGARGRGGRGARGAAPSRGRGAAPPRGRAGYSQRGGPGSARGVRGARGGAQQQRGRGQGKGVEAGP
          EDFQVGARGRGGRG.RGAAPSRG.GAAPP.GRAGYSQ.GGPGSARG..G.RGGAQQQRG.GQGKGVEA.P
Retrocopy EDFQVGARGRGGRGVRGAAPSRGHGAAPPCGRAGYSQKGGPGSARGIGGVRGGAQQQRGHGQGKGVEACP

Parental  DLLQ
          DLLQ
Retrocopy DLLQ

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	0.11 RPM	35.65 RPM
SRP017611_kidney	0.20 RPM	55.64 RPM
SRP017611_liver	0.08 RPM	41.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1683 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018345	1 retrocopy	retro_dnov_1927,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843,
Nomascus leucogenys	ENSNLEG00000012879	1 retrocopy	retro_nleu_162,
Oryctolagus cuniculus	ENSOCUG00000000601	1 retrocopy	retro_ocun_1683 ,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391,