RetrogeneDB ID: retro_ocun_886

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:17296449..17297727(-)
• Located in intron of: ENSOCUG00000011626

Retrocopy information

• Ensembl ID: ENSOCUG00000011909
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSOCUG00000011903
• Aliases: None
• Description: zinc finger CCCH-type containing 15 [Source:HGNC Symbol;Acc:29528]

Sequence

>retro_ocun_886
ATGCCCCCCAAGAAACAGGCTCAGGCCGGGGGCAGCAAAAAGGCGGAGCAGAAAAAGAAGGAAAAGATTATCGAAGACAA
AACTTTTGGTCTAAAGAATAAGAAAGGAGCAAAGCAAGAGAAGTTTATCAAAGCTGTCACTCATCAGGTTAAATTTGGTC
AACAAAATCCACGTCAGGTAGCACAAAGTGAAGCTGAGAAGAAATTGAAGAAAGATGACAAGAAGAAAGAATTACAGGAA
CTAAATGAGCTCTTCAAGCCTGTAGTTGCTGCTCAAAAAATTAGTAAAGGTGCAGATCCCAAGTCCGTAGTATGTGCATT
CTTCAAGCAAGGACAATGTACTAAAGGAGATAAGTGTAAATTCTTTCATGACTTGACTCTGGAGAGAAAATGTGAAAAGC
GGAGTGTTTACATTGATGCAAGAGATGAAGAACTTGAAAAGGATACTATGGATAATTGGGATGAGAAAAAGCTGGAAGAA
GTAGTGAACAAGAAGCACGGTGAGGCAGAAAAGAAAAAACCAAAAACTCAAATAGTATGCAAGCATTTCCTTGAAGCCAT
TGAAAACAACAAGTATGGCTGGTTTTGGGTTTGCCCTGGAGGGGGCGATAATTGCATGTATCGCCATGCACTTCCTCCTG
GATTTGTGTTGAAAAAAGACAAAAAGAAAGAAGAGAAAGAGGATGAAATTTCATTAGAAGATCTAATTGAAAGAGAGCGT
GCTGCCCTAGGCCCAAATGTTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAAAAAAGGAAAAGACAAGAAAAAAT
TGATAGACTTGAACAAGATATGGAAAGAAGAAAAGCTGACTTCAAAGCAGGCAAAGCACTAGTGATCAGTGGTCGTGAGG
TATTTGAATTTCGTCCTGAATTGGTCAATGATGATGATGAAGAAGCAGATGATACCCATTACACCCAAGGAACAGGTGGT
GATGAGGCTGATGATTCAATGAGCGTTAATGACATAGATTTAAGCCTGTACGTCCCAAGAGATGTAGATGAGACAGGTAT
TACTGTAGCCAGTCTTGAAAGATTCAGCACATATACTTCAGATAAAGACGAAAACAAATTAAGCGAAGCTTCTGGAGGTA
GGGCTGAAAATGGTGAAAGAAGTGATCTGGAAGAAGACAATGAAGGGGAAGGGCAGGAAAATGGAGCCATTGATGCCGTT
CCTGTTGATGAAAATCTTTTTACTGGGGAAGATCTGGATGAACTAGAAGAAGAATTAAACACACTTGATTTAGAAGAA

Alignment

ORF - retro_ocun_886 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
          MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQ.KFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
Retrocopy MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQEKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK

Parental  KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA
          KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKF.HDLTLERKCEKRSVYIDA
Retrocopy KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFFHDLTLERKCEKRSVYIDA

Parental  RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDNCMYRHA
          RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDNCMYRHA
Retrocopy RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDNCMYRHA

Parental  LPPGFVLKKDKKKEEKEDEISLEDLIERERAALGPNVTKITLESFLAWKKRKRQEKIDRLEQDMERRKAD
          LPPGFVLKKDKKKEEKEDEISLEDLIERERAALGPNVTKITLESFLAWKKRKRQEKIDRLEQDMERRKAD
Retrocopy LPPGFVLKKDKKKEEKEDEISLEDLIERERAALGPNVTKITLESFLAWKKRKRQEKIDRLEQDMERRKAD

Parental  FKAGKALVISGREVFEFRPELVNDDDEEADDTRYTQGTGGDEVDDSMSVNDIDLSLYVPRDVDETGITVA
          FKAGKALVISGREVFEFRPELVNDDDEEADDT.YTQGTGGDE.DDSMSVNDIDLSLYVPRDVDETGITVA
Retrocopy FKAGKALVISGREVFEFRPELVNDDDEEADDTHYTQGTGGDEADDSMSVNDIDLSLYVPRDVDETGITVA

Parental  SLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDELEEELN
          SLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDELEEELN
Retrocopy SLERFSTYTSDKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDELEEELN

Parental  TLDLEE
          TLDLEE
Retrocopy TLDLEE

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	0.33 RPM	34.11 RPM
SRP017611_kidney	0.10 RPM	32.13 RPM
SRP017611_liver	0.15 RPM	11.10 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_886 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Myotis lucifugus	ENSMLUG00000007741	2 retrocopies	retro_mluc_1494, retro_mluc_2467,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886 ,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,