RetrogeneDB ID: retro_ptro_2998

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390916.1:3146766..3147349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL19
• Ensembl ID: ENSPTRG00000009086
• Aliases: None
• Description: ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]

Sequence

>retro_ptro_2998
ATGAGGCTATTCAGGCTTCGGAAGAGGCTCGCCACGAGTGCCTCCACTGTAGCAAGAAGGTCTGGCTGGACCCCAGTGAG
ACCAGTGAAATCGTCAACGCCAACTCCCATCAGCAGATCCGGAGGCTGATCAAAGTTGGGCTGATCATCCACAAGCCTGT
GACTGTCCATTCCCAGGCTGGATGCCAGAAAAGCACCTTAGCCCACCAGAAGGGCAGGCACATGGGCACAGGTTAGCGCA
AGGGTACAGCCAATTTCCAAATGCCAGAGAAGGTCACTTGGATGAGGAGAATGAGGATTCTGCACTGGTTGTTTGGAAGA
TACCGTGAATCTAAGAAGACTGATCACCACATGTATCACAGCCTGTACCTGAAGGTGCAGGGGAATATGTTCACAAACAA
GCATATTCTCATGGAACACAACCACAAGCTGAAGGCAGACAAGGCCCACAAGAAGTTCCTGGCTGACCAGGCTGAGCCCG
CAGCTCTAAGACCAATAAAGCACGCAAGCTCCGTGAACAGCGCCTCCAGGCCAAAAAGAAGGAGATCATCAAGACTTTGT
CCAAGGAAGAAGAGACAAGAAAA

Alignment

ORF - retro_ptro_2998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSMLRLQKRLASSV-LRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLA
          M...RL.KRLA.S..L.C.KK.VWLDP.ET.EI.NANS.QQIR.LIK.GLII.KPVTVHS.A.C.K.TLA
Retrocopy MRLFRLRKRLATSA<LHCSKK-VWLDPSETSEIVNANSHQQIRRLIKVGLIIHKPVTVHSQAGCQKSTLA

Parental  RRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRILM
          ..KGRHMG.G.RKGTAN..MPEKVTWMRRMRIL..L..RYRESKK.D.HMYHSLYLKV.GN.F.NK.ILM
Retrocopy HQKGRHMGTG*RKGTANFQMPEKVTWMRRMRILHWLFGRYRESKKTDHHMYHSLYLKVQGNMFTNKHILM

Parental  EHIHKLKADKARKKLLADQAE-ARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
          EH.HKLKADKA.KK.LADQAE.AR.SKT..ARK.RE.RLQAKK.EIIKTLSKEEET.K
Retrocopy EHNHKLKADKAHKKFLADQAE<ARSSKTNKARKLREQRLQAKKKEIIKTLSKEEETRK

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	226.38 RPM
SRP007412_cerebellum	0.00 RPM	254.63 RPM
SRP007412_heart	0.00 RPM	225.62 RPM
SRP007412_kidney	0.00 RPM	560.51 RPM
SRP007412_liver	0.00 RPM	455.07 RPM
SRP007412_testis	0.00 RPM	166.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2998 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2998 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3933
Pongo abelii	retro_pabe_3299

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 122 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008520	4 retrocopies	retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus	ENSDNOG00000019742	7 retrocopies	retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Equus caballus	ENSECAG00000025080	6 retrocopies	retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Loxodonta africana	ENSLAFG00000018257	3 retrocopies	retro_lafr_1045, retro_lafr_479, retro_lafr_88,
Macaca mulatta	ENSMMUG00000004235	2 retrocopies	retro_mmul_283, retro_mmul_63,
Monodelphis domestica	ENSMODG00000012693	2 retrocopies	retro_mdom_53, retro_mdom_750,
Nomascus leucogenys	ENSNLEG00000000748	19 retrocopies	retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Pongo abelii	ENSPPYG00000008492	20 retrocopies	retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Pan troglodytes	ENSPTRG00000009086	22 retrocopies	retro_ptro_1180, retro_ptro_1385, retro_ptro_1642, retro_ptro_1676, retro_ptro_1786, retro_ptro_1806, retro_ptro_1930, retro_ptro_2036, retro_ptro_2214, retro_ptro_2279, retro_ptro_2311, retro_ptro_2645, retro_ptro_2709, retro_ptro_2865, retro_ptro_2998 , retro_ptro_305, retro_ptro_3109, retro_ptro_3179, retro_ptro_467, retro_ptro_525, retro_ptro_673, retro_ptro_737,
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,