RetrogeneDB ID: retro_hsap_4749

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:121672105..121673310(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232496
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL3
• Ensembl ID: ENSG00000100316
• Aliases: RPL3, ASC-1, L3, TARBP-B
• Description: ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]

Sequence

>retro_hsap_4749
ATATCTCACAGAAAGTTCTCCACTCCCAGACATGGGTCCCTCGGCTTCCTGCCTTGAAAGCACAATTGCAGGCATTGTGG
GAAGGTGAAGAGTTTCCCTAAGGATGACCCTTCCAAGCTGGTCCACCTCACAGCCTTCTTGAGATACAAGGTTGGCATGA
CCCACATCGTGAGGGGAAGTCAATAGGCCAGGATCCAAGGTGAGTACGAAGGAGGTGGTAGAGGCTGTGGCCATTGTGGA
GACAACCACCCATGGTGGTTGTGGGCATTGTGGGATATGGGGAAACCCTTCGAGGCATCTGGACTTTCAAGACCATCTTT
GCTGAGCACATCAGCAGTGAGTGCAAAAGGCGTTTCTATAAGAACTGACATAAATCTAAGAAGAAGCCCTTTACCAAGTA
CTGCAAGAAACGGCAGAAAGAGGATGGCAAAAAGCAGGTGTAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCA
TCCGCGTCATTGCCCACACCCAGATACGCCTGCTTCCTCTGCACCAGAAAGCCCACCTGATGGAGATCTAGGTGAACAGA
GGCACTGTGGCTGAGAAGCTGGACTGGGCCCAGAAGAGGCTCGAGCAGCAGGTACCTGTCAACCAAGTGTTTGGGCAAGA
TGAGATGATCAAAGTCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTTGTTGGCACACCACAAAGCTGC
CCCACAAGACCCACCGAGGCTTATGCAAGGTGGCCTGTATTGGGGCATGGCATCTTGCCCATGTGGCCTTCTCTGTGTCA
CACGCTGGTCAGAAAGGCTACCATCATGGCACTGAGATCAACAAGAAGATCTATAAGATCGGCCAGGGCTACCCTATCAT
GGACGGCAAACTGATCAAGAACAATGCCTCCATTGACTATGACCTGTCTGACAAGAGCATCAACTCTCTGGGTGGCTTTG
TCCACTGTGGCAAAGTGACCAATGACTTTGTCATGCTGAAAGGCTATGTGGTGGGAACCAAGAAGCAAGTGCTCACCCTC
TGCAAGTCCTTGCTGGTCCAGACCAAATGGCAGGCTCTGGAGAAGACTGACCTTAAGTTCACTGACACCACCTCCAACTT
TGGCCATTGCCACTTCCAGACCATGAAGAAGAAAGCATTCGTGAGACCACTCAAGAAAGACCAAATTGCAAAGGAAGAAG
GTGCT

Alignment

ORF - retro_hsap_4749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVR-EVDRPGSKVNK
          .SHRKFS.PRHGSLGFLP.K...RH.GKVKSFPKDDPSK.VHLTAFL.YK.GMTHIVR.EV.RPGSKV..
Retrocopy ISHRKFSTPRHGSLGFLP*KHNCRHCGKVKSFPKDDPSKLVHLTAFLRYKVGMTHIVR>EVNRPGSKVST

Parental  KEVVEAVTIVET-PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQ
          KEVVEAV.IVET.PPMVVVGIVGY.ET.RG..TFKT.FAEHIS.ECKRRFYKN.HKSKKK.FTKYCKK.Q
Retrocopy KEVVEAVAIVET>PPMVVVGIVGYGETLRGIWTFKTIFAEHISSECKRRFYKN*HKSKKKPFTKYCKKRQ

Parental  DEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVN
          .EDGKKQ..KDFSSMKKYCQVIRVIAHTQ.RLLPL.QK.AHLMEI.VN.GTVAEKLDWA..RLEQQVPVN
Retrocopy KEDGKKQV*KDFSSMKKYCQVIRVIAHTQIRLLPLHQK-AHLMEI*VNRGTVAEKLDWAQKRLEQQVPVN

Parental  QVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRT
          QVFGQDEMI.VIGVTKGKGYKGVTS.WHT.KLP.KTHRGL.KVACIGAWH.A.VAFSV..AGQKGYHH.T
Retrocopy QVFGQDEMIKVIGVTKGKGYKGVTSCWHTTKLPHKTHRGLCKVACIGAWHLAHVAFSVSHAGQKGYHHGT

Parental  EINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLR
          EINKKIYKIGQGY.I.DGKLIKNNAS.DYDLSDKSIN.LGGFVH.G.VTNDFVMLKG.VVGTKK.VLTL.
Retrocopy EINKKIYKIGQGYPIMDGKLIKNNASIDYDLSDKSINSLGGFVHCGKVTNDFVMLKGYVVGTKKQVLTLC

Parental  KSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
          KSLLVQTK..ALEK.DLKF.DTTS.FGH..FQTM..KKAF..PLKKD.IAKEEGA
Retrocopy KSLLVQTKWQALEKTDLKFTDTTSNFGHCHFQTM-KKKAFVRPLKKDQIAKEEGA

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
bodymap2_adipose	0.00 RPM	1680.36 RPM
bodymap2_adrenal	0.02 RPM	1617.45 RPM
bodymap2_brain	0.05 RPM	431.16 RPM
bodymap2_breast	0.00 RPM	1202.87 RPM
bodymap2_colon	0.00 RPM	1954.47 RPM
bodymap2_heart	0.00 RPM	136.94 RPM
bodymap2_kidney	0.00 RPM	828.19 RPM
bodymap2_liver	0.00 RPM	515.37 RPM
bodymap2_lung	0.00 RPM	1395.71 RPM
bodymap2_lymph_node	0.00 RPM	1623.01 RPM
bodymap2_ovary	0.00 RPM	2926.00 RPM
bodymap2_prostate	0.00 RPM	1872.53 RPM
bodymap2_skeletal_muscle	0.00 RPM	319.11 RPM
bodymap2_testis	0.00 RPM	1379.42 RPM
bodymap2_thyroid	0.00 RPM	1149.27 RPM
bodymap2_white_blood_cells	0.00 RPM	1856.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4749 was not detected

EST

No EST(s) were mapped for retro_hsap_4749 retrocopy.

TSS

No TSS is located nearby retro_hsap_4749 retrocopy 5' end.

Lab

retro_hsap_4749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4749 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3163
Gorilla gorilla	retro_ggor_2955
Pongo abelii	retro_pabe_3696

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 109 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010853	1 retrocopy	retro_amel_1115,
Bos taurus	ENSBTAG00000003228	3 retrocopies	retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris	ENSCAFG00000001346	1 retrocopy	retro_cfam_97,
Callithrix jacchus	ENSCJAG00000016276	6 retrocopies	retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Dasypus novemcinctus	ENSDNOG00000001121	4 retrocopies	retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Erinaceus europaeus	ENSEEUG00000014661	2 retrocopies	retro_eeur_488, retro_eeur_557,
Echinops telfairi	ENSETEG00000011380	5 retrocopies	retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus	ENSFCAG00000005820	1 retrocopy	retro_fcat_1809,
Homo sapiens	ENSG00000100316	9 retrocopies	retro_hsap_1341, retro_hsap_2403, retro_hsap_2529, retro_hsap_3328, retro_hsap_3448, retro_hsap_3638, retro_hsap_3889, retro_hsap_4081, retro_hsap_4749 ,
Gorilla gorilla	ENSGGOG00000002326	10 retrocopies	retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii	ENSMEUG00000009789	26 retrocopies	retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Microcebus murinus	ENSMICG00000015832	1 retrocopy	retro_mmur_1307,
Myotis lucifugus	ENSMLUG00000023711	1 retrocopy	retro_mluc_810,
Monodelphis domestica	ENSMODG00000009539	2 retrocopies	retro_mdom_380, retro_mdom_408,
Mustela putorius furo	ENSMPUG00000013271	3 retrocopies	retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,