RetrogeneDB ID: retro_ocun_1595

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018707:2057634..2058626(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000007693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSOCUG00000014147
• Aliases: None
• Description: cysteine and histidine-rich domain (CHORD) containing 1 [Source:HGNC Symbol;Acc:14525]

Sequence

>retro_ocun_1595
ATGGCTCTGCTGTGCTACAACCGGGGCTGCGGCCAGCGCTTCGATCCTGAGAATAACTCTGATGATGCCTGCACATACCA
CCCAGGTGTTCTAGTCTTTCATGATGCATTCAAGGGTTGGTCTTGCTGTAAGAGAAGAACAACTGATTTTTCTGATTTCT
TAAGCATTGTAGGCTGTACAAAAGGTAGGCATAATAATGAGAAGCTGCCTGAACCAGTCAAGCCTGAACTGAAGACCACA
GAAAAGAAAGAACTATCTGAATTGAAACCCAAATTTCAGGAGCACGTCATTCAAGCCCCTAAACCGGTAGAAACAATAAA
AAGGACAAGTCCAGATGAACCAATGACAAATTTGGAATTAAAAATACCTGCCTCCCTAAAACAAGCACTTGATAAACTTA
AACTATCATCAGGGATTGAAGAGAGAAGAAAGAAGAAGACAATGATGAAATTAAGATTGGAACCTCATGTGAAAATGGAG
GGTGTTCAAAGACATACCAGGGTCAAGAGAGTCTAGAAGAAGTCTGTCTATATCATTCTGGAGTACCTATTTTTCATGAA
GGGATGAAATACTGGAGCTGTTGCAGAAGAAAAACCTCTGACTTTAATACATTCTTAGCCCAGGAGGGCTGTACGACAGG
AAAACACTTGTGGACTAAAAAGGATGATGGTAAAAAAGTTGTTCCATGTAGACACGACTGGCATCAGACTGGAGGTGAAC
TCACCATTTCAGTATATGCTAAAAATTCACTTCCAGAATTTAGTCGAGTAGAAGCAAAGAGTGCATTGTTAAATGTTCAC
ATTGTATTTGAAAGAGAGAAGGAATTTCATCAAAATGTGAAATTATGGGGTGTGATTGATGTAAAACAAAGTTATGTAAC
TATGACTGCAACAAAGATTGAAATCACCATGAGAAAAGCTGAACCTATGCAGTGGACGAGCCTTGAACTGCCTGTGACCA
AAAAGCCTGAAAAGCAGAAAGATATTTCAGAG

Alignment

ORF - retro_ocun_1595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALLCYNRGCGQRFDPENNSDDACTYHPGVPVFHDALKGWSCCKRRTTDFSDFLSIVGCTKGRHNNEKPP
          MALLCYNRGCGQRFDPENNSDDACTYHPGV.VFHDA.KGWSCCKRRTTDFSDFLSIVGCTKGRHNNEK.P
Retrocopy MALLCYNRGCGQRFDPENNSDDACTYHPGVLVFHDAFKGWSCCKRRTTDFSDFLSIVGCTKGRHNNEKLP

Parental  EPVKPEVKTTEKKELSELKPKFQEHIIQAPKPVETIKRPSPDEPMTNLELKISASLKQALDKLKLSSGIE
          EPVKPE.KTTEKKELSELKPKFQEH.IQAPKPVETIKR.SPDEPMTNLELKI.ASLKQALDKLKLSSGIE
Retrocopy EPVKPELKTTEKKELSELKPKFQEHVIQAPKPVETIKRTSPDEPMTNLELKIPASLKQALDKLKLSSGIE

Parental  E-EKKEEDNDEIKIGTSCKNGGCSKTYQGQESLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQE
          E.EKKEEDNDEIKIGTSC.NGGCSKTYQGQESLEEVC.YHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQE
Retrocopy E<EKKEEDNDEIKIGTSCENGGCSKTYQGQESLEEVCLYHSGVPIFHEGMKYWSCCRRKTSDFNTFLAQE

Parental  GCTTGKHLWTKKDDGKKVVPCRHDWHQTGGEVTISVYAKNSLPELSRVEANSTLLNVHIVFEREKEFHQN
          GCTTGKHLWTKKDDGKKVVPCRHDWHQTGGE.TISVYAKNSLPE.SRVEA.S.LLNVHIVFEREKEFHQN
Retrocopy GCTTGKHLWTKKDDGKKVVPCRHDWHQTGGELTISVYAKNSLPEFSRVEAKSALLNVHIVFEREKEFHQN

Parental  VKLWGVIDVKRSYVTMTATKIEITMRKAEPMQWASLELPMTKKPEKQKDISD
          VKLWGVIDVK.SYVTMTATKIEITMRKAEPMQW.SLELP.TKKPEKQKDIS.
Retrocopy VKLWGVIDVKQSYVTMTATKIEITMRKAEPMQWTSLELPVTKKPEKQKDISE

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	21.30 RPM
SRP017611_kidney	0.00 RPM	12.26 RPM
SRP017611_liver	0.00 RPM	4.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1595 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1595 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024, retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595 ,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959, retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,