RetrogeneDB ID: retro_pabe_1898

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:25045158..25045467(-)
• Located in intron of: ENSPPYG00000011701

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36
• Ensembl ID: ENSPPYG00000009431
• Aliases: None
• Description: 60S ribosomal protein L36 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAZ9]

Sequence

>retro_pabe_1898
ATGGCTCTGCTTTATCCTACAGCCATGGGCCTCAACAAGGGCCACAAGGTGACCAAGAATGTGAGCAAGCCCAGGCCCAG
CTGCCATCGCAGGTGCCTGACCAAACACACCAAGTTCATGCGGGTTATGATCTGAGAGGTGTGTGGCTTCACCCTGTATG
GGCAGCATCCCATGGAATAGCTCAAGGTCTCCAAGGACAAATGGGCCTTCAAGTTCATCAAGAAAAAGGTGGGAACACAC
ATCCACACCAAGAGGAAGTAGGAGGAGCTGCACAATGTCCTGGCCACCATAAGGAAAGCCGCTGCCAAG

Alignment

ORF - retro_pabe_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 98.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALRYPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFAPYERRAMELLKVSKDKRAL
          MAL.YP.A.GLNKGHKVTKNVSKPR.S..R..LTKHTKF.R.MI.EVCGF..Y....ME.LKVSKDK.A.
Retrocopy MALLYPTAMGLNKGHKVTKNVSKPRPSCHRRCLTKHTKFMRVMI*EVCGFTLYGQHPME*LKVSKDKWAF

Parental  KFIKKRVGTHIRAKRKREELSNVLAAMRKAAAK
          KFIKK.VGTHI..KRK.EEL.NVLA..RKAAAK
Retrocopy KFIKKKVGTHIHTKRK*EELHNVLATIRKAAAK

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	32.23 RPM
SRP007412_cerebellum	0.00 RPM	22.37 RPM
SRP007412_heart	0.00 RPM	21.13 RPM
SRP007412_kidney	0.00 RPM	80.91 RPM
SRP007412_liver	0.03 RPM	81.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1898 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1898 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2577
Pan troglodytes	retro_ptro_1506
Gorilla gorilla	retro_ggor_1613

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 129 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012349	6 retrocopies	retro_amel_1222, retro_amel_1581, retro_amel_1935, retro_amel_748, retro_amel_799, retro_amel_835,
Bos taurus	ENSBTAG00000001794	3 retrocopies	retro_btau_139, retro_btau_238, retro_btau_81,
Callithrix jacchus	ENSCJAG00000017072	2 retrocopies	retro_cjac_280, retro_cjac_52,
Cavia porcellus	ENSCPOG00000022839	3 retrocopies	retro_cpor_1317, retro_cpor_1343, retro_cpor_857,
Dasypus novemcinctus	ENSDNOG00000005163	8 retrocopies	retro_dnov_19, retro_dnov_2160, retro_dnov_311, retro_dnov_313, retro_dnov_457, retro_dnov_578, retro_dnov_595, retro_dnov_631,
Echinops telfairi	ENSETEG00000012943	15 retrocopies	retro_etel_1168, retro_etel_1199, retro_etel_1315, retro_etel_1336, retro_etel_139, retro_etel_1396, retro_etel_1425, retro_etel_1432, retro_etel_1528, retro_etel_2168, retro_etel_342, retro_etel_575, retro_etel_78, retro_etel_908, retro_etel_922,
Felis catus	ENSFCAG00000011838	5 retrocopies	retro_fcat_1152, retro_fcat_1168, retro_fcat_1216, retro_fcat_406, retro_fcat_94,
Homo sapiens	ENSG00000130255	13 retrocopies	retro_hsap_1059, retro_hsap_1440, retro_hsap_2000, retro_hsap_2434, retro_hsap_2577, retro_hsap_3051, retro_hsap_3248, retro_hsap_3769, retro_hsap_3892, retro_hsap_396, retro_hsap_4211, retro_hsap_4742, retro_hsap_534,
Gorilla gorilla	ENSGGOG00000015365	11 retrocopies	retro_ggor_1514, retro_ggor_1613, retro_ggor_180, retro_ggor_2211, retro_ggor_2535, retro_ggor_2620, retro_ggor_34, retro_ggor_487, retro_ggor_60, retro_ggor_82, retro_ggor_885,
Latimeria chalumnae	ENSLACG00000015161	1 retrocopy	retro_lcha_47,
Macropus eugenii	ENSMEUG00000002743	4 retrocopies	retro_meug_1318, retro_meug_176, retro_meug_261, retro_meug_283,
Monodelphis domestica	ENSMODG00000001275	2 retrocopies	retro_mdom_1353, retro_mdom_148,
Mustela putorius furo	ENSMPUG00000006166	6 retrocopies	retro_mputfur_1423, retro_mputfur_150, retro_mputfur_1562, retro_mputfur_747, retro_mputfur_749, retro_mputfur_773,
Mus musculus	ENSMUSG00000057863	9 retrocopies	retro_mmus_151, retro_mmus_1601, retro_mmus_1900, retro_mmus_1912, retro_mmus_193, retro_mmus_2864, retro_mmus_3379, retro_mmus_38, retro_mmus_652,
Otolemur garnettii	ENSOGAG00000027049	12 retrocopies	retro_ogar_1348, retro_ogar_18, retro_ogar_184, retro_ogar_2256, retro_ogar_2278, retro_ogar_2332, retro_ogar_2537, retro_ogar_2592, retro_ogar_3278, retro_ogar_358, retro_ogar_795, retro_ogar_888,
Pongo abelii	ENSPPYG00000009431	12 retrocopies	retro_pabe_1194, retro_pabe_137, retro_pabe_1639, retro_pabe_1792, retro_pabe_1834, retro_pabe_1898 , retro_pabe_216, retro_pabe_3081, retro_pabe_3173, retro_pabe_318, retro_pabe_3443, retro_pabe_3688,
Rattus norvegicus	ENSRNOG00000033473	5 retrocopies	retro_rnor_11, retro_rnor_17, retro_rnor_170, retro_rnor_369, retro_rnor_687,
Sarcophilus harrisii	ENSSHAG00000013492	8 retrocopies	retro_shar_185, retro_shar_347, retro_shar_543, retro_shar_557, retro_shar_592, retro_shar_615, retro_shar_716, retro_shar_819,
Sus scrofa	ENSSSCG00000030010	2 retrocopies	retro_sscr_849, retro_sscr_960,
Ictidomys tridecemlineatus	ENSSTOG00000020518	2 retrocopies	retro_itri_43, retro_itri_593,