RetrogeneDB ID: retro_ptro_1546

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:61573027..61573461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000008742
• Aliases: None
• Description: None

Sequence

>retro_ptro_1546
ATGAAGTACAATCCCTTTGTGACTTCTGACTGAAGCAAGAACTGCAAAAGGCATTTCAATGCACCTTCCCACACTCGCAG
AAAGATTATGTCCTCCCCTCTTTCCAAAGAGCTGAGACAAAAGTACAATGTTCGATCAAAGACCATCCAAAAAGATGACG
AGGTTCAGGTTGTGCGAGGACACTGTAAGGGTCAGCAAATTGGCCAAATAATCCAGGTTTACAGGAAGAAATATGCCATC
TACATTGAACGGGTGCAGTGGGAAAAGGCTAACAGCATAGCTGTCCCTGTGGGCATTCACCCAGCAAGGTGGTTATCACT
AGACTAAAACTTGACAAAGGCCACAAAAAGATCCTTGAACGGAAAGCCAAATCTCGCCAAGTAGGAAAAGAAAATGGAAA
ATACAAGAAAGAAACAATAGGGAAGGTGCAGGAA

Alignment

ORF - retro_ptro_1546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          MK.NPFVTSD.SKN.KRHFNAPSH.RRKIMSSPLSKELRQKYNVRS..I.KDDEVQVVRGH.KGQQIG..
Retrocopy MKYNPFVTSD*SKNCKRHFNAPSHTRRKIMSSPLSKELRQKYNVRSKTIQKDDEVQVVRGHCKGQQIGQI

Parental  VQVYRKKYVIYIERVQREKANGTTVHVGIH-PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEET
          .QVYRKKY.IYIERVQ.EKAN...V.VGIH.PSKVVITRLKLDK..KKILERKAKSRQVGKE.GKYK.ET
Retrocopy IQVYRKKYAIYIERVQWEKANSIAVPVGIH<PSKVVITRLKLDKGHKKILERKAKSRQVGKENGKYKKET

Parental  IEKMQE
          I.K.QE
Retrocopy IGKVQE

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	147.43 RPM
SRP007412_cerebellum	0.00 RPM	66.10 RPM
SRP007412_heart	0.00 RPM	45.91 RPM
SRP007412_kidney	0.00 RPM	142.42 RPM
SRP007412_liver	0.00 RPM	66.42 RPM
SRP007412_testis	0.42 RPM	30.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1546 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1546 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2108
Macaca mulatta	retro_mmul_992

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 144 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Cavia porcellus	ENSCPOG00000001315	10 retrocopies	retro_cpor_1009, retro_cpor_1161, retro_cpor_1346, retro_cpor_1421, retro_cpor_1503, retro_cpor_1526, retro_cpor_167, retro_cpor_522, retro_cpor_585, retro_cpor_858,
Equus caballus	ENSECAG00000015757	4 retrocopies	retro_ecab_429, retro_ecab_473, retro_ecab_515, retro_ecab_609,
Felis catus	ENSFCAG00000011259	13 retrocopies	retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Macropus eugenii	ENSMEUG00000009891	7 retrocopies	retro_meug_1239, retro_meug_1538, retro_meug_1607, retro_meug_1827, retro_meug_262, retro_meug_322, retro_meug_534,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Mustela putorius furo	ENSMPUG00000007988	12 retrocopies	retro_mputfur_1003, retro_mputfur_1146, retro_mputfur_1385, retro_mputfur_1428, retro_mputfur_1595, retro_mputfur_251, retro_mputfur_365, retro_mputfur_395, retro_mputfur_488, retro_mputfur_522, retro_mputfur_643, retro_mputfur_685,
Mus musculus	ENSMUSG00000060938	21 retrocopies	retro_mmus_1325, retro_mmus_1444, retro_mmus_1506, retro_mmus_1642, retro_mmus_1866, retro_mmus_1978, retro_mmus_2011, retro_mmus_2218, retro_mmus_2435, retro_mmus_2540, retro_mmus_2673, retro_mmus_3078, retro_mmus_3174, retro_mmus_320, retro_mmus_3270, retro_mmus_3291, retro_mmus_3361, retro_mmus_384, retro_mmus_556, retro_mmus_900, retro_mmus_939,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Oryctolagus cuniculus	ENSOCUG00000006538	11 retrocopies	retro_ocun_1125, retro_ocun_1290, retro_ocun_1442, retro_ocun_1484, retro_ocun_1515, retro_ocun_1621, retro_ocun_1917, retro_ocun_529, retro_ocun_542, retro_ocun_589, retro_ocun_803,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes	ENSPTRG00000008742	3 retrocopies	retro_ptro_1546 , retro_ptro_2510, retro_ptro_73,
Rattus norvegicus	ENSRNOG00000004214	3 retrocopies	retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus	ENSSTOG00000021923	6 retrocopies	retro_itri_1113, retro_itri_1145, retro_itri_1206, retro_itri_1262, retro_itri_1670, retro_itri_811,