RetrogeneDB ID: retro_ocun_38

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:73382820..73383951(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000663
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTC1
• Ensembl ID: ENSOCUG00000004074
• Aliases: None
• Description: actin, alpha, cardiac muscle 1 [Source:HGNC Symbol;Acc:143]

Sequence

>retro_ocun_38
ATGACCGATGATGAGCTGTCTGCCTTAGTAGTGGATAATGGGTCAGGGATGTGCAAGGCAGGCTTCGGTGGTGACGATGC
CCCCCGGGCTGTGTTCCCCTCCATGGTGGGGCGCCCCCGACACCAAGGGGTCATGGTAGGCATGGGCCAGAAGGACTGCT
ATGTAGGGGATGAGGCCCAAAGCAAGAGAGGCATCCTGACCCTACAGTATCCCATTGAGCACGGAGTAGTCACCAACTGG
GACGACATGGAGAAGATCTGGTACCACACTTTCTACAACGAGCTCCGTGTAGCACCAGATGAGCATCCCATCCTCCTCAC
TGAAGCACCCCTCAACCCCAAGATCAACCGGGAAAAGATGACTCAGATCATGTTCGAGGCCTTCAACACACCTGCCATGT
ATGTGGCTATCCAAGCTGTGCTGTCCCTCTATGCTTCTGGACGAACCACAGGCATCGTAATGGATTCCGGGGACGGGGTC
ACTCACACCGTGCCCATCTATGAAGGCTACGCCCTGCCCCACGCTATCCTACGTCTGGACCTGGCAGGCAGAGATCTGAC
GGATTACCTCATGAAGACCCTGACGGAAAGAGGCTATAACTTCACCACGACGGCTGAGCGAGAGATTGTGCGGGATGTCA
AGGAGAAGCTGTGCTATGTGGCCCTAGACTTTGAGCAAGAGATGATCGGTGCAGCAGCATCTTCCTCACTGGAGAGAAGC
TATGAGCTTCCTGATGGGCAGGTGATCACCATTGGGAACGAGCGCTTCCGATGCCCTGAAGCCATTTTCCAGCCTTCCTT
TCTGGGCATCGAGTCCAGTGGAATCCATGAGACAACCTTCAACTCCACCATGAAGTGTGATGTGGATATTCGCAAGGATT
TATATGCCAACACAGTGTTGTCTGGAGGCAGCACCATGTACCCAGGCATTGCTGACCGGATGCAGAAGGAGATCATGACC
CTGGCCCCCAGCACCATGAAAGTCAAGATCATTGCCCCCCCAGAACGCAAGTATTCCGTTTGGATTGGGGGCTCCATCCT
GGCCAGCCTCTCCACGTTCCAGCAGATGTGGATCAGTAAGCAGGAATATGATGAAGCTGGTCCTCCTATTGTTCATAGAA
AATGCTTCTGA

Alignment

ORF - retro_ocun_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          D.E..ALV.DNGSG..KAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTL.YPI
Retrocopy DDELSALVVDNGSGMCKAGFGGDDAPRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLQYPI

Parental  EHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLS
          EHG..TNWDDMEKIW.HTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FN.PAMYVAIQAVLS
Retrocopy EHGVVTNWDDMEKIWYHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVLS

Parental  LYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRD
          LYASGRTTGIV.DSGDGVTH.VPIYEGYALPHAI.RLDLAGRDLTDYLMK.LTERGY.F.TTAEREIVRD
Retrocopy LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKTLTERGYNFTTTAEREIVRD

Parental  IKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNS
          .KEKLCYVALDFE.EM..AA.SSSLE.SYELPDGQVITIGNERFRCPE..FQPSF.G.ES.GIHETT.NS
Retrocopy VKEKLCYVALDFEQEMIGAAASSSLERSYELPDGQVITIGNERFRCPEAIFQPSFLGIESSGIHETTFNS

Parental  IMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
          .MKCD.DIRKDLYAN.VLSGG.TMYPGIADRMQKEI..LAPSTMK.KIIAPPERKYSVWIGGSILASLST
Retrocopy TMKCDVDIRKDLYANTVLSGGSTMYPGIADRMQKEIMTLAPSTMKVKIIAPPERKYSVWIGGSILASLST

Parental  FQQMWISKQEYDEAGPSIVHRKCF
          FQQMWISKQEYDEAGP.IVHRKCF
Retrocopy FQQMWISKQEYDEAGPPIVHRKCF

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	4.69 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_38 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_38 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_38 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_38
Pan troglodytes	retro_ptro_53
Gorilla gorilla	retro_ggor_1297
Pongo abelii	retro_pabe_86
Callithrix jacchus	retro_cjac_243
Mus musculus	retro_mmus_283
Rattus norvegicus	retro_rnor_351
Bos taurus	retro_btau_903
Canis familiaris	retro_cfam_934
Equus caballus	retro_ecab_98

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000011801	1 retrocopy	retro_lcha_19,
Oryctolagus cuniculus	ENSOCUG00000004074	1 retrocopy	retro_ocun_38 ,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000006318	1 retrocopy	retro_pabe_1317,