RetrogeneDB ID: retro_ocun_98

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:65602315..65603623(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000016910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: AP2M1
• Ensembl ID: ENSOCUG00000004556
• Aliases: None
• Description: adaptor-related protein complex 2, mu 1 subunit [Source:HGNC Symbol;Acc:564]

Sequence

>retro_ocun_98
ATGATCGGAGGCTTATTCATCTATAATCACAAGGGGGAGGTGCTCATCTCCCGGGTCTACCGAGATGACATAGGGAGGAA
TGCAGTGGACGCCTTCCGGGTCAATGTTATCCATGCCCGGCAGCAGGTGCGCAGCCCCGTCACCAACATTGCTCGCACCA
GCTTCTTCCATGTTAAGTGGTCCAACATCTGGCTGGCCGCTGTCACCAAGCAGAATGTCAACGCTGCCATGGTCTTCGAA
TTCCTCTATAAGATGTGTGACGTAATGGCTGCCTACTTTGCCAAGATCAGCGAAGAAAACATCAAGAACAATTTTGTGCT
CATATACGAGATGCTAGATGAGATCCTGGACTTTGGCTACCCACAGAACTCTGAGACAGGCGCTCTGAAAACCTTCATCA
CCCAGCAGGGCATCAAGAGTCAGCATCAGACAAAAGAAGAACAGTCCCAGATCACCAGACAGGTGACTGGGCAGATCGGC
TGGCGGCGAGAAGGCATCACGTATCGCCGGAATGAGCTCTTCTTGGATGTGCTGGAGAGTGTGAACCTACTGATGTCCCC
ACAGGGGCAGGTGCTGAGTGCCCATGTGTCCGGCCGGGTGGTGATGAAGAGCTACCTGAGTGGCATGCCCGAGTGCAAGT
TTGGGATGAATGACAAGATTGTAATTGAAAAGCAAGGCAGAGGCACAGCTGATGAAACAAGCAAGAGCGGGAAGCAATCA
ATTGCCATTGATGACTGCACCTTCCACCAGTGTGTGCGACTCAGCAAGTTTGACTCTGAACGCAGCATCAGCTTCATCCC
ACCAGATGGAGAGTTTGAGCTCATGAGGTATCGCACCACCAAGGACATCATCCTTCCTTTCCGGGTGATTCCGCTGGTAC
GGGAAGTGGGACGCACCAAACTGGAGGTAAAGGTGGTCATCAAGTCCAACTTTAAGCCCTCACTGCTGGCTCAGAAAATT
GAGGTGCGGATTCCAACCCCACTGAACACAAGTGGTGTGCAGGTGATCTGCATGAAGGGGAAGGCCAAGTATAAGGCCAG
TGAGAACGCCATCGTATGGAAGATCAAGCGCATGGCAGGCATGAAGGAATCACGGATCAGCGGAGAGATTGAGCTTCTGC
CCACCAATGACAAGAAAAAATGGGCCCGACCTCCTATTTCCATGAATTTTGAGGTGCCATTTGCGCCTTCTGGCCTCAAG
GTGCGCTACTTGAAGGTGTTTGAACCGAAGCTGAACTACAGCGACCACGACGTCATCGAATGGGTGCGCTACATTGGCCG
CAGCGGCATTTACGAGACCCGCTGCTAG

Alignment

ORF - retro_ocun_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTK
          MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVK.SNIWLAAVTK
Retrocopy MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKWSNIWLAAVTK

Parental  QNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKS
          QNVNAAMVFEFLYKMCDVMAAYF.KISEENIKNNFVLIYE.LDEILDFGYPQNSETGALKTFITQQGIKS
Retrocopy QNVNAAMVFEFLYKMCDVMAAYFAKISEENIKNNFVLIYEMLDEILDFGYPQNSETGALKTFITQQGIKS

Parental  QHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP
          QHQTKEEQSQIT.QVTGQIGWRREGI.YRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP
Retrocopy QHQTKEEQSQITRQVTGQIGWRREGITYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP

Parental  ECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTT
          ECKFGMNDKIVIEKQG.GTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTT
Retrocopy ECKFGMNDKIVIEKQGRGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTT

Parental  KDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA
          KDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA
Retrocopy KDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA

Parental  IVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
          IVWKIKRMAGMKES.IS.EIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVI.
Retrocopy IVWKIKRMAGMKESRISGEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIE

Parental  WVRYIGRSGIYETRC
          WVRYIGRSGIYETRC
Retrocopy WVRYIGRSGIYETRC

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	12.97 RPM	416.67 RPM
SRP017611_kidney	5.47 RPM	219.94 RPM
SRP017611_liver	0.69 RPM	67.29 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_98 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_98 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_98 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020106	1 retrocopy	retro_btau_1156,
Canis familiaris	ENSCAFG00000012257	2 retrocopies	retro_cfam_1923, retro_cfam_2028,
Erinaceus europaeus	ENSEEUG00000006073	1 retrocopy	retro_eeur_47,
Echinops telfairi	ENSETEG00000004759	1 retrocopy	retro_etel_2124,
Macropus eugenii	ENSMEUG00000002558	1 retrocopy	retro_meug_43,
Mus musculus	ENSMUSG00000022841	2 retrocopies	retro_mmus_1873, retro_mmus_1914,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98 ,
Oryctolagus cuniculus	ENSOCUG00000024334	1 retrocopy	retro_ocun_1089,
Otolemur garnettii	ENSOGAG00000012286	1 retrocopy	retro_ogar_1110,
Rattus norvegicus	ENSRNOG00000001709	1 retrocopy	retro_rnor_2342,
Tarsius syrichta	ENSTSYG00000006101	1 retrocopy	retro_tsyr_1873,
Tursiops truncatus	ENSTTRG00000008493	1 retrocopy	retro_ttru_522,