RetrogeneDB ID: retro_opri_292

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4766:204168..204716(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FTH1
• Ensembl ID: ENSOPRG00000010734
• Aliases: None
• Description: ferritin, heavy polypeptide 1 [Source:HGNC Symbol;Acc:3976]

Sequence

>retro_opri_292
ATGACGACCCCTTCCCCCTTGCAGGTGCGCCAGAACTACTGCCAGGACTGGAGACTGCCATCAACCGCCAGATCAACCTG
GAGCCGTACGCCTCCTATGTCTACCTGTCGGTGTCTTACTACTTTGACCCTGATGATGTGGCTTTGAAGAACTTCGCCAA
ATACTTCCTCCACCGGTCTCATGAAGGAGCGGGAACATGCAGAGAAACTGATGCAGCTGCAGAACCAGAGCGGTGGCCGG
AGCTTTCTTCAGGACATCTAGAAACCAGATCGTGATGACTGGGAGAATGGGCTGAAGGCACTGGAGTGCGCATTGCACCT
GGAACAAAGTGTCAGTCAGTCACTACTGGAACTGTACAAGCTGGCCCCTGACAAGAATGATCCCTCCTTGTGTGACTTCA
TCGGGGCTCATTTACTGGATGAGCAGGTGAAAGCTGTCAAGGAACTGGGCAGCCATGTAACCAACTTGCTCAGGATGGGA
GGCCTACAGCTGGCATGGCAGTGTATTTCTTCGCCCAGTACATCCTCGGACACTGTTATAACCAGACC

Alignment

ORF - retro_opri_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTTASPSQVRQNYHQD-SEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHE-EREHAE
          MTT.SP.QVRQNY.QD..E.AINRQINLE.YASYVYLS.SYYFD.DDVALKNFAKYFLH.SHE.EREHAE
Retrocopy MTTPSPLQVRQNYCQD<LETAINRQINLEPYASYVYLSVSYYFDPDDVALKNFAKYFLHRSHE>EREHAE

Parental  KLMKLQNQRGGRIFLQDIKKPDRDDWENGLNAMECALHLEQSVNQSLLELHKLATDKNDPHLCDFIETHY
          KLM.LQNQ.GGR.FLQDI.KPDRDDWENGL.A.ECALHLEQSV.QSLLEL.KLA.DKNDP.LCDFI..H.
Retrocopy KLMQLQNQSGGRSFLQDI*KPDRDDWENGLKALECALHLEQSVSQSLLELYKLAPDKNDPSLCDFIGAHL

Parental  LDEQVKAIKELGDHVTNLRRMGA-PTAGMAEYLFDKHTLGHSDNQS
          LDEQVKA.KELG.HVTNL.RMG..PTAGMA.Y.F....LGH..NQ.
Retrocopy LDEQVKAVKELGSHVTNLLRMGG<PTAGMAVYFFAQYILGHCYNQT

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_292 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 18 parental genes, and 203 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016831	1 retrocopy	retro_amel_115,
Bos taurus	ENSBTAG00000011184	10 retrocopies	retro_btau_1151, retro_btau_121, retro_btau_1255, retro_btau_1473, retro_btau_1708, retro_btau_1745, retro_btau_256, retro_btau_595, retro_btau_673, retro_btau_959,
Canis familiaris	ENSCAFG00000015901	1 retrocopy	retro_cfam_150,
Callithrix jacchus	ENSCJAG00000019089	16 retrocopies	retro_cjac_1570, retro_cjac_1634, retro_cjac_2115, retro_cjac_2233, retro_cjac_230, retro_cjac_232, retro_cjac_2320, retro_cjac_2531, retro_cjac_278, retro_cjac_2843, retro_cjac_2857, retro_cjac_485, retro_cjac_519, retro_cjac_699, retro_cjac_767, retro_cjac_804,
Cavia porcellus	ENSCPOG00000026586	3 retrocopies	retro_cpor_1309, retro_cpor_15, retro_cpor_157,
Dasypus novemcinctus	ENSDNOG00000017128	83 retrocopies	retro_dnov_1017, retro_dnov_1074, retro_dnov_1078, retro_dnov_110, retro_dnov_1179, retro_dnov_1188, retro_dnov_1196, retro_dnov_1201, retro_dnov_1205, retro_dnov_1271, retro_dnov_1352, retro_dnov_1356, retro_dnov_1369, retro_dnov_1397, retro_dnov_1415, retro_dnov_1425, retro_dnov_1446, retro_dnov_1489, retro_dnov_1526, retro_dnov_1535, retro_dnov_1554, retro_dnov_1565, retro_dnov_162, retro_dnov_1627, retro_dnov_1640, retro_dnov_1777, retro_dnov_1787, retro_dnov_1792, retro_dnov_1827, retro_dnov_1851, retro_dnov_1865, retro_dnov_1875, retro_dnov_189, retro_dnov_197, retro_dnov_2005, retro_dnov_2065, retro_dnov_2093, retro_dnov_2097, retro_dnov_2109, retro_dnov_2124, retro_dnov_2136, retro_dnov_2154, retro_dnov_2173, retro_dnov_220, retro_dnov_2216, retro_dnov_2231, retro_dnov_2241, retro_dnov_2251, retro_dnov_2356, retro_dnov_2388, retro_dnov_2399, retro_dnov_242, retro_dnov_2443, retro_dnov_2444, retro_dnov_2454, retro_dnov_2476, retro_dnov_2483, retro_dnov_2489, retro_dnov_2511, retro_dnov_2528, retro_dnov_2554, retro_dnov_2579, retro_dnov_2607, retro_dnov_2626, retro_dnov_2646, retro_dnov_304, retro_dnov_383, retro_dnov_409, retro_dnov_422, retro_dnov_471, retro_dnov_517, retro_dnov_52, retro_dnov_55, retro_dnov_589, retro_dnov_61, retro_dnov_661, retro_dnov_675, retro_dnov_722, retro_dnov_726, retro_dnov_810, retro_dnov_864, retro_dnov_890, retro_dnov_994,
Felis catus	ENSFCAG00000007382	1 retrocopy	retro_fcat_887,
Gorilla gorilla	ENSGGOG00000027722	7 retrocopies	retro_ggor_1313, retro_ggor_153, retro_ggor_1671, retro_ggor_1858, retro_ggor_2835, retro_ggor_64, retro_ggor_726,
Latimeria chalumnae	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Loxodonta africana	ENSLAFG00000004824	12 retrocopies	retro_lafr_106, retro_lafr_1080, retro_lafr_1129, retro_lafr_138, retro_lafr_321, retro_lafr_433, retro_lafr_523, retro_lafr_53, retro_lafr_624, retro_lafr_717, retro_lafr_760, retro_lafr_966,
Myotis lucifugus	ENSMLUG00000025726	16 retrocopies	retro_mluc_1030, retro_mluc_1142, retro_mluc_1211, retro_mluc_1354, retro_mluc_1464, retro_mluc_1769, retro_mluc_1984, retro_mluc_2002, retro_mluc_2091, retro_mluc_212, retro_mluc_2635, retro_mluc_361, retro_mluc_532, retro_mluc_556, retro_mluc_850, retro_mluc_885,
Monodelphis domestica	ENSMODG00000007582	9 retrocopies	retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Oryctolagus cuniculus	ENSOCUG00000014108	4 retrocopies	retro_ocun_1172, retro_ocun_1179, retro_ocun_1598, retro_ocun_93,
Ochotona princeps	ENSOPRG00000002492	10 retrocopies	retro_opri_187, retro_opri_270, retro_opri_422, retro_opri_43, retro_opri_551, retro_opri_618, retro_opri_702, retro_opri_785, retro_opri_883, retro_opri_886,
Ochotona princeps	ENSOPRG00000010734	7 retrocopies	retro_opri_1219, retro_opri_292 , retro_opri_558, retro_opri_689, retro_opri_816, retro_opri_818, retro_opri_936,
Pongo abelii	ENSPPYG00000003173	12 retrocopies	retro_pabe_1034, retro_pabe_1186, retro_pabe_2410, retro_pabe_2483, retro_pabe_2484, retro_pabe_249, retro_pabe_3351, retro_pabe_3406, retro_pabe_35, retro_pabe_3713, retro_pabe_47, retro_pabe_479,
Sus scrofa	ENSSSCG00000014540	9 retrocopies	retro_sscr_1045, retro_sscr_168, retro_sscr_286, retro_sscr_359, retro_sscr_498, retro_sscr_581, retro_sscr_78, retro_sscr_906, retro_sscr_949,
Ictidomys tridecemlineatus	ENSSTOG00000014521	1 retrocopy	retro_itri_250,