RetrogeneDB ID: retro_ptro_900

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:29696945..29697351(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27
• Ensembl ID: ENSPTRG00000009232
• Aliases: None
• Description: ribosomal protein L27 [Source:HGNC Symbol;Acc:10328]

Sequence

>retro_ptro_900
ATGGGCAAGTTCGTGAAACCTCGGAAAGTGGTGTTTGTCCTGGCTGGATGCTACTCCAGACACAAAGCTGTCATCGTGAA
GAACATTGATGATGGCACCTCAGATCGCCCCTACAGCCATGCCCTGGTGGCTGGAATTGACCACTATCCCTGCAAAGTAA
GAGCTGCCATGGGCAAGAAGAAGATCACCAAGAGGTCAAAGATCAAGTCTTTTGTGAAAGTTTATAACTAATCACCTAAT
GCCCACAAGGTACTCTGTGGCTATCCTCTTGGACAAAACTGTCATTAATAAGGATGTCTGCAGACACCCTGCTCTTAAAC
CCAAGGCTGGACAAGAAGCCAAGATCAAGTTTGAAAAGAGGTACAAGACGGGCAAGAACAAGTGGTTCTTCCAGAAGCTG
CAGTTT

Alignment

ORF - retro_ptro_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRY-PRKVTAAMGKKKIAKRSKIK
          MGKF.KP.KVV.VLAG.YS..KAVIVKNIDDGTSDRPYSHALVAGID.Y.P.K............R....
Retrocopy MGKFVKPRKVVFVLAGCYSRHKAVIVKNIDDGTSDRPYSHALVAGIDHY>PAK*ELPWARRR-SPRGQRS

Parental  SFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF
          S.......NHLMPTRYSV.I.LDKTV.NKDV.R.PALK.KA..EAK.KFE.RYKTGKNKWFFQKL.F
Retrocopy SLL*KFITNHLMPTRYSVAILLDKTVINKDVCRHPALKPKAGQEAKIKFEKRYKTGKNKWFFQKLQF

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	0.04 RPM	138.35 RPM
SRP007412_cerebellum	0.00 RPM	236.06 RPM
SRP007412_heart	0.03 RPM	189.74 RPM
SRP007412_kidney	0.08 RPM	287.80 RPM
SRP007412_liver	0.13 RPM	319.45 RPM
SRP007412_testis	0.00 RPM	55.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_900 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_900 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1312

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 112 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000200	3 retrocopies	retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus	ENSBTAG00000017441	6 retrocopies	retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris	ENSCAFG00000014630	6 retrocopies	retro_cfam_1193, retro_cfam_2109, retro_cfam_339, retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus	ENSCJAG00000013067	9 retrocopies	retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Felis catus	ENSFCAG00000013142	6 retrocopies	retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Homo sapiens	ENSG00000131469	6 retrocopies	retro_hsap_1161, retro_hsap_1312, retro_hsap_2112, retro_hsap_2204, retro_hsap_238, retro_hsap_3787,
Gorilla gorilla	ENSGGOG00000026039	6 retrocopies	retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana	ENSLAFG00000014220	3 retrocopies	retro_lafr_443, retro_lafr_739, retro_lafr_965,
Microcebus murinus	ENSMICG00000014214	5 retrocopies	retro_mmur_1340, retro_mmur_1498, retro_mmur_1542, retro_mmur_673, retro_mmur_695,
Myotis lucifugus	ENSMLUG00000004119	1 retrocopy	retro_mluc_359,
Macaca mulatta	ENSMMUG00000008090	7 retrocopies	retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica	ENSMODG00000015128	1 retrocopy	retro_mdom_1141,
Mus musculus	ENSMUSG00000063316	2 retrocopies	retro_mmus_223, retro_mmus_277,
Nomascus leucogenys	ENSNLEG00000011901	2 retrocopies	retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus	ENSOCUG00000003872	1 retrocopy	retro_ocun_263,
Otolemur garnettii	ENSOGAG00000003940	14 retrocopies	retro_ogar_1091, retro_ogar_1297, retro_ogar_1478, retro_ogar_1692, retro_ogar_1887, retro_ogar_2189, retro_ogar_2354, retro_ogar_2625, retro_ogar_2687, retro_ogar_2915, retro_ogar_3207, retro_ogar_3294, retro_ogar_3381, retro_ogar_618,
Pan troglodytes	ENSPTRG00000009232	6 retrocopies	retro_ptro_127, retro_ptro_1673, retro_ptro_208, retro_ptro_2569, retro_ptro_794, retro_ptro_900 ,
Pteropus vampyrus	ENSPVAG00000008817	4 retrocopies	retro_pvam_1084, retro_pvam_1231, retro_pvam_25, retro_pvam_509,
Rattus norvegicus	ENSRNOG00000020674	8 retrocopies	retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sarcophilus harrisii	ENSSHAG00000012042	4 retrocopies	retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,
Tarsius syrichta	ENSTSYG00000003167	12 retrocopies	retro_tsyr_1032, retro_tsyr_1154, retro_tsyr_1711, retro_tsyr_2036, retro_tsyr_381, retro_tsyr_476, retro_tsyr_602, retro_tsyr_787, retro_tsyr_816, retro_tsyr_822, retro_tsyr_95, retro_tsyr_989,