RetrogeneDB ID: retro_ptro_2134

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:28595018..28595668(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSPTRG00000018085
• Aliases: None
• Description: ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]

Sequence

>retro_ptro_2134
ATGAGCAGCAAAGTCTCTCGCGACACCCAGTGGGAGGCAGTGCAGAAAGTTCTGCACAGGAACCAGCGCTAGCACCGCAA
ATTCCTGGAGACGGTGTAGTTGCAGATCAGCTTGAAGAAGTATGACCCCCAGAAGGACAAGCGCTTCTCGGGCACCATCA
GGCTTAAGTCCACTCCCCGCCCCAAGTTCTCTGTGTGTGTTCTGGCGGACCAGTAGCACTGTGACGAGGCCAAGGCCATG
GATATCCCCCACATGGACATTGAGGCGCTGAAAAAACTCAACAAGAATAAAAAACTGGTCAAGAAGCTGGCCAAGAAGTA
TGATGCGTTTTTGGCCTCAGAGTCCCTGATCGAGCAGATTCCACGAATCCTCGGCCCACGTCTAAATAAGGCAGGAAAGT
TCCCTTCCCTGCTCACACACAACGAAAACATGGTGGCCAAAGTGGATGAGGTGAAGTTCACAATCAAGTTCCAAATGAAG
AAGGTGTTATATCTGGCTGTAGCTGTTGGTCACGTGAAGATGACAGACGATGAGCTTGTGGATAACATTCACCTGGCTGT
CCACTTCTTGGTGTCATTGCTTAAGAAATACTGGCAGAATGTCTGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCA
GCGCCTATAT

Alignment

ORF - retro_ptro_2134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGD
          MSSKVSRDT..EAV..VLH.NQR..RKFLETV.LQISLK.YDPQKDKRFSGT.RLKSTPRPKFSVCVL.D
Retrocopy MSSKVSRDTQWEAVQKVLHRNQR*HRKFLETV*LQISLKKYDPQKDKRFSGTIRLKSTPRPKFSVCVLAD

Parental  QQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTH
          Q.HCDEAKA.DIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLI.QIPRILGP.LNKAGKFPSLLTH
Retrocopy Q*HCDEAKAMDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIEQIPRILGPRLNKAGKFPSLLTH

Parental  NENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNV-RALYIKST
          NENMVAKVDEVK.TIKFQMKKVL.LAVAVGHVKMTDDELV.NIHLAV.FLVSLLKK.WQNV..ALYIKST
Retrocopy NENMVAKVDEVKFTIKFQMKKVLYLAVAVGHVKMTDDELVDNIHLAVHFLVSLLKKYWQNV<LALYIKST

Parental  MGKPQRLY
          MGKPQRLY
Retrocopy MGKPQRLY

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	0.13 RPM	141.85 RPM
SRP007412_cerebellum	0.00 RPM	162.07 RPM
SRP007412_heart	0.03 RPM	92.39 RPM
SRP007412_kidney	0.08 RPM	279.14 RPM
SRP007412_liver	0.16 RPM	160.59 RPM
SRP007412_testis	0.00 RPM	43.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2134 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2134 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2759

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001318	18 retrocopies	retro_cfam_1118, retro_cfam_1200, retro_cfam_1222, retro_cfam_124, retro_cfam_1501, retro_cfam_1775, retro_cfam_1867, retro_cfam_2002, retro_cfam_2141, retro_cfam_281, retro_cfam_337, retro_cfam_347, retro_cfam_413, retro_cfam_847, retro_cfam_907, retro_cfam_911, retro_cfam_920, retro_cfam_986,
Echinops telfairi	ENSETEG00000013325	2 retrocopies	retro_etel_1974, retro_etel_326,
Gorilla gorilla	ENSGGOG00000028140	10 retrocopies	retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Myotis lucifugus	ENSMLUG00000000080	10 retrocopies	retro_mluc_1053, retro_mluc_1526, retro_mluc_1611, retro_mluc_1815, retro_mluc_1963, retro_mluc_1964, retro_mluc_2519, retro_mluc_751, retro_mluc_902, retro_mluc_918,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Oryctolagus cuniculus	ENSOCUG00000004065	2 retrocopies	retro_ocun_130, retro_ocun_4,
Pan troglodytes	ENSPTRG00000018085	13 retrocopies	retro_ptro_1157, retro_ptro_1293, retro_ptro_142, retro_ptro_167, retro_ptro_1892, retro_ptro_2041, retro_ptro_2134 , retro_ptro_2193, retro_ptro_2681, retro_ptro_269, retro_ptro_2729, retro_ptro_2737, retro_ptro_994,
Pteropus vampyrus	ENSPVAG00000002763	9 retrocopies	retro_pvam_1107, retro_pvam_1223, retro_pvam_123, retro_pvam_1294, retro_pvam_1440, retro_pvam_345, retro_pvam_722, retro_pvam_775, retro_pvam_906,
Rattus norvegicus	ENSRNOG00000000505	4 retrocopies	retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Ictidomys tridecemlineatus	ENSSTOG00000023366	3 retrocopies	retro_itri_1097, retro_itri_524, retro_itri_847,