RetrogeneDB ID: retro_ocun_1306

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:87231618..87232755(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSOCUG00000008193
• Aliases: None
• Description: actin, alpha 2, smooth muscle, aorta (ACTA2), mRNA [Source:RefSeq mRNA;Acc:NM_001101682]

Sequence

>retro_ocun_1306
GCTCAGCTCACCATGGATGACGATATCGCCTCGCTCGTGGTCGACAATGGCTCCGGCATGTGCAAGGCCGGCTTCACGGG
CGACGATGCCCCCCGGGCCGTCTTCCCCTCCATCGTGGGGCGTCCGCGGCAGCAGGGTGTGATGGTGGGCATGGGCCAGA
AGGACTCGTACGTGGGCGACGAGGCCCAGAGCAAGCGTGGCACCCTGATGCTCAAGTACCCCATCGAGCACGGCATCGTG
ACCAACTGGGACGACATGGAGAAGATCTGGCACCACACCTTCTACAACGAGCTGCGCGTGGCCCCCGAGGAGCACCCGGT
GCTGCTGACCGAGGCCCCCCTGAACCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTCGAGACGTTCAACACGC
CGGCCATGTACGTGGCCATCCAGGCCGTGCTGTCCCTGTACGCCTCTGGCCGCACCACAGGCATCGTGACGGACTCCGGC
GACGGGGTCACCCACACGGTGCCCATCTACGAGGGCTACGCGCTGCCGCACGCCTTCCTGCGTCTGGACCTGGATGGTCG
GGACCTGACCGACTACCTCATGAAGATCCTCACGGAGCACGGCTACAGCTTCACCACCACCGCAGAGCGCGAGATCATGC
GCTACATCAAGGAGGAGCTGTGCTACGTGGCGCTGGACTTCGAGCAGGAGATGGCCAGGGCCGCGTCCTCCTGCTCCCTG
GAGAAGAGCTACGAGCTGCCCGACAGCCAGGTCATCACCATCGGCAACGAGCACTTCTGCTGCCCCGAGGTGCTGTTCCA
GCCCTCCTTCCTGGGCATGGAGTCGTGCGGCATCCACGAGACCACCTTCAACTCGATCATGGAGTGCGACGTGGACATCC
GCAAGGACCTGTACGCCAACATGGTGCTGTCAGGCTGCACCACCATGTACCCCGGCATCGCCGACCACACACAGAAGGAG
ATCACTGCCCTGGCACCCAGCACCATGAAGATCAAGATCATCGCTCCCACCGAGCGCAAGTACTCGGTGTGAATCGGCGG
CTCCATCCTGGCCTCGCTGTCCACGTTCCAGCAGATGTGGATCAGCAAGCAGGAGTACGACGAGTCGGGCCCCTCCATCG
TGCACCGCAAGTGTTTC

Alignment

ORF - retro_ocun_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.34 %
• Parental protein coverage: 80.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAMCEEEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILT
          A......D...LV.DNGSG.CKAGF.GDDAPRAVFPSIVGRPR.QGVMVGMGQKDSYVGDEAQSKRG.L.
Retrocopy AQLTMDDDIASLVVDNGSGMCKAGFTGDDAPRAVFPSIVGRPRQQGVMVGMGQKDSYVGDEAQSKRGTLM

Parental  LKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAI
          LKYPIEHGI.TNWDDMEKIWHH.FYNELRVAPEEHP.LLTEAPLNPKANREKMTQIMFETFN.PAMYVAI
Retrocopy LKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAI

Parental  QAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAER
          QAVLSLYASGRTTGIV.DSGDGVTH.VPIYEGYALPHA..RLDL.GRDLTDYLMKILTE.GYSF.TTAER
Retrocopy QAVLSLYASGRTTGIVTDSGDGVTHTVPIYEGYALPHAFLRLDLDGRDLTDYLMKILTEHGYSFTTTAER

Parental  EIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHE
          EI.R.IKE.LCYVALDFE.EMA.AASS.SLEKSYELPD.QVITIGNE.F.CPE.LFQPSF.GMES.GIHE
Retrocopy EIMRYIKEELCYVALDFEQEMARAASSCSLEKSYELPDSQVITIGNEHFCCPEVLFQPSFLGMESCGIHE

Parental  TTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSIL
          TT.NSIM.CD.DIRKDLYAN.VLSG.TTMYPGIAD..QKEITALAPSTMKIKIIAP.ERKYSV.IGGSIL
Retrocopy TTFNSIMECDVDIRKDLYANMVLSGCTTMYPGIADHTQKEITALAPSTMKIKIIAPTERKYSV*IGGSIL

Parental  ASLSTFQQMWISKQEYDEAGPSIVHRKCF
          ASLSTFQQMWISKQEYDE.GPSIVHRKCF
Retrocopy ASLSTFQQMWISKQEYDESGPSIVHRKCF

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	65.95 RPM	17.99 RPM
SRP017611_kidney	59.19 RPM	42.77 RPM
SRP017611_liver	33.07 RPM	22.20 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1306 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
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	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,