RetrogeneDB ID: retro_hsap_2594

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:43172411..43173302(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000234009
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL5
• Ensembl ID: ENSG00000122406
• Aliases: RPL5, DBA6, L5
• Description: ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]

Sequence

>retro_hsap_2594
ATGGGGTTTGTTAAAGTTGTTAAGAATAAGGCCTACTTTAACAGATACCAAGTGAAATTTAGAAGACGACGAGAGGGTAA
AACTGATTACTATGCTCGGAAACGCTTGGTGATACAGGATAAAAATAAATACAACACACCCAAGTATAGGATGATTGTTC
GTGTAACTGACAGAGATATCATTTGTCAGATTGCTTATGCCCGTATAGAGGGGGATATGATAGTCTGCGCGGCATATGCA
CACGAACTGCCAAAATACGGTGTGAAGGTTGGCCCGACAAATTATGCTGCTGCATATTGTACTGGCCTGCTGCTGGCCCG
CAGGCTTCTTGATAGGTTTGGCATGGACAAGATCTATGACGGCCAAGTGGAGGTGACTGGCGATAAATACAATGTGGAAA
GTACTGATGGTCAGCCAGGTGCCTTCACCTGCTGTATGGATGCAGGTCTTGCCAGAACTACCACTGGCAATAAAGTTTTT
GGCGCCCTGAAGGGAGTTGTGGATGGAGGCTTGTCTGTCCCTCACAGCACCAAATGATTCCCTGGTTATGATTCTGAAAG
CAAGGAATTTAATGCAGGAGTACACCAGAAGCACTTCATGGGCCAGAATGTTGCAGATTACATGCGCTACTTAATGGAAG
AAGATGACGATGCTTACAAGAAACAGTTCTCTCAATACATAAAGAACAGCGTAACTCCAGACATGATGGAGGAGATGTAT
AAGAAAGCTCATGCTGCTATACGAGAGAATCCAGTCTATGAAAAGAAGCCCAAGAAAGAAGTTAAAAAGGAGAGGTGGAA
CCTTCCCAAAATGCCCCTTGCTCAGAAGAAGGATCAGGTAGCTCAAAAGAAGGCAAGCTTCCTCAGAGCTCAGGAGCGGG
CTGCTGAGAGC

Alignment

ORF - retro_hsap_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
          MGFVKVVKNKAYF.RYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVT.RDIICQIAYARIE
Retrocopy MGFVKVVKNKAYFNRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTDRDIICQIAYARIE

Parental  GDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPG
          GDMIVCAAYAHELPKYGVKVG.TNYAAAYCTGLLLARRLL.RFGMDKIY.GQVEVTGD.YNVES.DGQPG
Retrocopy GDMIVCAAYAHELPKYGVKVGPTNYAAAYCTGLLLARRLLDRFGMDKIYDGQVEVTGDKYNVESTDGQPG

Parental  AFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRY
          AFTC..DAGLARTTTGNKVFGALKG.VDGGLS.PHSTK.FPGYDSESKEFNA.VH.KH.MGQNVADYMRY
Retrocopy AFTCCMDAGLARTTTGNKVFGALKGVVDGGLSVPHSTK*FPGYDSESKEFNAGVHQKHFMGQNVADYMRY

Parental  LMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRV
          LMEED.DAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKK.RWN.PKM.LAQKKD.V
Retrocopy LMEEDDDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKERWNLPKMPLAQKKDQV

Parental  AQKKASFLRAQERAAES
          AQKKASFLRAQERAAES
Retrocopy AQKKASFLRAQERAAES

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	0.14 RPM	831.47 RPM
bodymap2_adrenal	0.33 RPM	1088.69 RPM
bodymap2_brain	0.02 RPM	287.02 RPM
bodymap2_breast	0.21 RPM	690.73 RPM
bodymap2_colon	0.37 RPM	1255.57 RPM
bodymap2_heart	0.06 RPM	286.90 RPM
bodymap2_kidney	1.86 RPM	467.21 RPM
bodymap2_liver	0.17 RPM	264.66 RPM
bodymap2_lung	0.05 RPM	964.12 RPM
bodymap2_lymph_node	0.22 RPM	1025.32 RPM
bodymap2_ovary	0.48 RPM	2109.24 RPM
bodymap2_prostate	1.04 RPM	1546.91 RPM
bodymap2_skeletal_muscle	0.15 RPM	345.73 RPM
bodymap2_testis	0.38 RPM	860.64 RPM
bodymap2_thyroid	0.21 RPM	950.21 RPM
bodymap2_white_blood_cells	0.55 RPM	1265.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2594 was not detected

EST

No EST(s) were mapped for retro_hsap_2594 retrocopy.

TSS

No TSS is located nearby retro_hsap_2594 retrocopy 5' end.

Lab

retro_hsap_2594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2594 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1519

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 141 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002852	1 retrocopy	retro_eeur_620,
Echinops telfairi	ENSETEG00000009889	8 retrocopies	retro_etel_1044, retro_etel_1089, retro_etel_1103, retro_etel_1264, retro_etel_2028, retro_etel_64, retro_etel_785, retro_etel_814,
Homo sapiens	ENSG00000122406	30 retrocopies	retro_hsap_1266, retro_hsap_138, retro_hsap_1469, retro_hsap_1539, retro_hsap_1588, retro_hsap_1767, retro_hsap_183, retro_hsap_1989, retro_hsap_2143, retro_hsap_2385, retro_hsap_2594 , retro_hsap_2600, retro_hsap_2777, retro_hsap_2962, retro_hsap_3105, retro_hsap_3178, retro_hsap_3181, retro_hsap_3209, retro_hsap_3430, retro_hsap_3520, retro_hsap_3941, retro_hsap_4048, retro_hsap_4104, retro_hsap_486, retro_hsap_590, retro_hsap_632, retro_hsap_646, retro_hsap_742, retro_hsap_780, retro_hsap_827,
Gorilla gorilla	ENSGGOG00000002699	24 retrocopies	retro_ggor_1129, retro_ggor_1172, retro_ggor_1206, retro_ggor_1342, retro_ggor_1343, retro_ggor_1656, retro_ggor_1934, retro_ggor_2052, retro_ggor_2130, retro_ggor_2178, retro_ggor_2243, retro_ggor_2318, retro_ggor_233, retro_ggor_2380, retro_ggor_264, retro_ggor_2649, retro_ggor_2715, retro_ggor_2755, retro_ggor_457, retro_ggor_521, retro_ggor_553, retro_ggor_622, retro_ggor_647, retro_ggor_996,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus	ENSMLUG00000008956	1 retrocopy	retro_mluc_925,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Nomascus leucogenys	ENSNLEG00000010500	2 retrocopies	retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Otolemur garnettii	ENSOGAG00000013246	6 retrocopies	retro_ogar_1164, retro_ogar_134, retro_ogar_1627, retro_ogar_2374, retro_ogar_2633, retro_ogar_707,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pongo abelii	ENSPPYG00000001152	32 retrocopies	retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Pan troglodytes	ENSPTRG00000000963	30 retrocopies	retro_ptro_1038, retro_ptro_1068, retro_ptro_1184, retro_ptro_1326, retro_ptro_139, retro_ptro_1519, retro_ptro_1524, retro_ptro_1568, retro_ptro_169, retro_ptro_1744, retro_ptro_1878, retro_ptro_2005, retro_ptro_2241, retro_ptro_2262, retro_ptro_2264, retro_ptro_2329, retro_ptro_2391, retro_ptro_2674, retro_ptro_2742, retro_ptro_2785, retro_ptro_2941, retro_ptro_3027, retro_ptro_366, retro_ptro_433, retro_ptro_460, retro_ptro_470, retro_ptro_528, retro_ptro_577, retro_ptro_866, retro_ptro_997,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	7.36 RPM
CEU_NA11843	16.83 RPM
CEU_NA11930	9.03 RPM
CEU_NA12004	16.83 RPM
CEU_NA12400	12.35 RPM
CEU_NA12751	9.01 RPM
CEU_NA12760	8.44 RPM
CEU_NA12827	10.28 RPM
CEU_NA12872	9.50 RPM
CEU_NA12873	11.45 RPM
FIN_HG00183	8.84 RPM
FIN_HG00277	7.58 RPM
FIN_HG00315	13.22 RPM
FIN_HG00321	8.46 RPM
FIN_HG00328	9.09 RPM
FIN_HG00338	13.52 RPM
FIN_HG00349	14.08 RPM
FIN_HG00375	10.05 RPM
FIN_HG00377	11.77 RPM
FIN_HG00378	8.90 RPM
GBR_HG00099	8.75 RPM
GBR_HG00111	14.14 RPM
GBR_HG00114	8.76 RPM
GBR_HG00119	7.18 RPM
GBR_HG00131	6.09 RPM
GBR_HG00133	8.25 RPM
GBR_HG00134	9.89 RPM
GBR_HG00137	8.22 RPM
GBR_HG00142	9.75 RPM
GBR_HG00143	10.59 RPM
TSI_NA20512	12.58 RPM
TSI_NA20513	10.01 RPM
TSI_NA20518	13.24 RPM
TSI_NA20532	8.71 RPM
TSI_NA20538	7.83 RPM
TSI_NA20756	9.49 RPM
TSI_NA20765	8.47 RPM
TSI_NA20771	11.26 RPM
TSI_NA20786	8.76 RPM
TSI_NA20798	8.26 RPM
YRI_NA18870	7.85 RPM
YRI_NA18907	9.08 RPM
YRI_NA18916	11.30 RPM
YRI_NA19093	8.25 RPM
YRI_NA19099	7.48 RPM
YRI_NA19114	10.64 RPM
YRI_NA19118	11.29 RPM
YRI_NA19213	5.43 RPM
YRI_NA19214	7.99 RPM
YRI_NA19223	10.29 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).