RetrogeneDB ID: retro_itri_982

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393355.1:7967764..7968312(+)
• Located in intron of: ENSSTOG00000011114

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSSTOG00000011327
• Aliases: None
• Description: ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]

Sequence

>retro_itri_982
GTACAAGGATATCTGAAAAACAACCCAGCTCTGGAGAAACAATTGCCTCATATCCAGGGGAATGTGAGCTTTGTGTTCAC
CTAGGAGGACCTCATTGAGATCAGGGACATACTGTTGGCCAGGTTTCAGTTGCTGCCCATTGCTGGTGCCATTGCACCTT
GTGAAGTCACTGTGCCAGCTCAGAACAGTGGTCTGGAGCCCAAGAAGACTTTCTTCTTCCAGGCTTTAGGCATCACTACT
AAAATCTGCAGGGGCACCATTGAAATCGTGAGTAATGTGTAACTGATAAAGACTAGAGACAAAGTTGGAGCCAGTGAAGC
TACCCTGCTGAATGTGCTGACAATCTTTCCTTTCTCCTGTGGGCGAATCCAGTACATGTTTGACAATGGCAGCATCTACA
GTCCTGAAGTGCTTGACATCACAGAGAAGACTCTGCATTCTTGCTTCCTGGAGAGTGACTGCAGTGTTGCTATTGTTTGT
CTGCAGATTCCAACTATTGGATAATGCCTCATTCTGTCATCAGTGGGTGTAAGTGGGTCCTGGCTTTG

Alignment

ORF - retro_itri_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.28 %
• Parental protein coverage: 58.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRGHLENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEK
          ..G.L.NNPALEK.LPHI.GNV.FVFT.EDL.EIRD.LLA........AGAIAPCEVTVPAQN.GL.P.K
Retrocopy VQGYLKNNPALEKQLPHIQGNVSFVFT*EDLIEIRDILLA-RFQLLPIAGAIAPCEVTVPAQNSGLEPKK

Parental  TSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVL
          T.FFQALGITTKI.RGTIEI.S.V.LIKT.DKVGASEATLLN.L.I.PFS.G..IQ..FDNGSIY.PEVL
Retrocopy TFFFQALGITTKICRGTIEIVSNV*LIKTRDKVGASEATLLNVLTIFPFSCGR-IQYMFDNGSIYSPEVL

Parental  DITEETLHSRFLEGVRNVASVCLQIGYPTVA-SVPHSIINGYKRVLAL
          DITE.TLHS.FLE....VA.VCLQI..PT.....PHS.I.G.K.VLAL
Retrocopy DITEKTLHSCFLESDCSVAIVCLQI--PTIG<IMPHSVISGCKWVLAL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_982 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_982 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005144	4 retrocopies	retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris	ENSCAFG00000010227	5 retrocopies	retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Felis catus	ENSFCAG00000013354	1 retrocopy	retro_fcat_441,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Myotis lucifugus	ENSMLUG00000001970	11 retrocopies	retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mustela putorius furo	ENSMPUG00000003055	4 retrocopies	retro_mputfur_1632, retro_mputfur_362, retro_mputfur_426, retro_mputfur_910,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Nomascus leucogenys	ENSNLEG00000000292	11 retrocopies	retro_nleu_1080, retro_nleu_1365, retro_nleu_1419, retro_nleu_1470, retro_nleu_1551, retro_nleu_1639, retro_nleu_1686, retro_nleu_1722, retro_nleu_2058, retro_nleu_2927, retro_nleu_3095,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Pteropus vampyrus	ENSPVAG00000003110	3 retrocopies	retro_pvam_114, retro_pvam_62, retro_pvam_745,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Ictidomys tridecemlineatus	ENSSTOG00000011327	4 retrocopies	retro_itri_1155, retro_itri_276, retro_itri_331, retro_itri_982 ,
Tarsius syrichta	ENSTSYG00000009732	7 retrocopies	retro_tsyr_1133, retro_tsyr_130, retro_tsyr_1376, retro_tsyr_1429, retro_tsyr_727, retro_tsyr_75, retro_tsyr_84,
Vicugna pacos	ENSVPAG00000012156	2 retrocopies	retro_vpac_234, retro_vpac_45,