RetrogeneDB ID: retro_ocun_983

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:67771644..67772423(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSOCUG00000006368
• Aliases: None
• Description: mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]

Sequence

>retro_ocun_983
AGGACGACAATAGGGCGGCAAGTTTGTCAGCTTCCTGGTCTCTCTTGTTACGCTCAGCACATTGCCAGCATTGATGGGAG
GCGTGGGTTGTTCACAGCCTTAACTCCTGGACTGTGTCCAGGAATCCTTGGAACCGTGATCCATGGTAAAGTTGTACAGC
ATTACCAGGCGTGTGACAAGGTTGAGGACGTGGGACCTGGACATGCACAGAAGGAAGTCTCATCTTCCTTTGACCAAGTT
ATCAAAGCGACAACGCAAGAGATAACCGCTCGATCTGCTGCTACCCTCCTCACACATGCCTTCCACGTGAGCGCGCTGAG
ATCATGGTACAATTCATTGGCAGAGAATCCAAGTACTCTGGGCTTGTGACTCCATAGCAACCATCTGTTGGGAAGAAGGC
ATCCTAGGAATTTTTGCAGGTCTTACTCCTCACCTCCTGGGTGACATAATTCTTTGCGGCTCTGTAACTCACTGGCGTCC
TCATCAGTGCCTGTGCACTGGACAGTAGGGTGTCTACCTTGAATGAAAGGAAGAGTTACTCCCAAGTGTCACAGGATTTT
TTGCCAGTATGTTGACCTGCCCCTCTGTGCTTGAGTCTAATCTTACGGCTGTCAACAACTGTGGGCTTCTGGTGGATGCC
CTTACTCCCCCGGATGTACTTCTTGGATAGATTGCTGGTGCATGCTACAAAAAGACAGAAACATGAGCAGAGGAAGGAGC
TTGCTTTTCCGGAAGGTCCACTTTGGAAGACTTATTGTTGTGACCTGAAAATGTTAATG

Alignment

ORF - retro_ocun_983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 86.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RNIFGRQVCQLPGLFCYAQHIASIDGRRGLFTGLTPRLCSGVLGTVVHGKVLQHYQECDKVEDLGPGNAQ
          R...GRQVCQLPGL.CYAQHIASIDGRRGLFT.LTP.LC.G.LGTV.HGKV.QHYQ.CDKVED.GPG.AQ
Retrocopy RTTIGRQVCQLPGLSCYAQHIASIDGRRGLFTALTPGLCPGILGTVIHGKVVQHYQACDKVEDVGPGHAQ

Parental  KDVSSSFDRVIKETTREMIARSAATLITHPFHVITLRS-MVQFIGRESKYCVPSGLY-DSIVTIYREEGI
          K.VSSSFD.VIK.TT.E..ARSAATL.TH.FHV..LRS.MVQFIGRESKY...SGL..DSI.TI..EEGI
Retrocopy KEVSSSFDQVIKATTQEITARSAATLLTHAFHVSALRS<MVQFIGRESKY---SGLV<DSIATICWEEGI

Parental  LGFFAGLIPRLLGDII-SLWLCNSLA-YLVNTYALDSGVSTMNEMKSYSQ-AVTGFFASMLTYPFVLVSN
          LG.FAGL.P.LLGDII.SL.LCNSLA..L....ALDS.VST.NE.KSYSQ..VTGFFASMLT.P.VL.SN
Retrocopy LGIFAGLTPHLLGDII<SLRLCNSLA<VLISACALDSRVSTLNERKSYSQ<SVTGFFASMLTCPSVLESN

Parental  LMAVNNCGL-AGGCPPYSPIYTSWIDCWCMLQKEGNMSRGNSLFFRKVPFG-KTYCCDLKMLM
          L.AVNNCGL..GGC.PYSP..TSWIDCWCMLQK..NMSRG.SL.FRKV.FG.KTYCCDLKMLM
Retrocopy LTAVNNCGL<SGGC-PYSPGCTSWIDCWCMLQKDRNMSRGRSLLFRKVHFG<KTYCCDLKMLM

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	116.56 RPM
SRP017611_kidney	0.00 RPM	137.74 RPM
SRP017611_liver	0.00 RPM	81.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_983 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_983 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018742	1 retrocopy	retro_btau_1321,
Choloepus hoffmanni	ENSCHOG00000008473	1 retrocopy	retro_chof_2162,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003, retro_cjac_3812,
Dasypus novemcinctus	ENSDNOG00000001221	1 retrocopy	retro_dnov_1867,
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furo	ENSMPUG00000003852	1 retrocopy	retro_mputfur_312,
Mus musculus	ENSMUSG00000027282	1 retrocopy	retro_mmus_2657,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus	ENSOCUG00000006368	2 retrocopies	retro_ocun_1197, retro_ocun_983 ,
Otolemur garnettii	ENSOGAG00000011607	1 retrocopy	retro_ogar_2578,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes	ENSPTRG00000003573	2 retrocopies	retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus	ENSPVAG00000007348	1 retrocopy	retro_pvam_954,
Sorex araneus	ENSSARG00000001399	1 retrocopy	retro_sara_705,
Sus scrofa	ENSSSCG00000013232	3 retrocopies	retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,