RetrogeneDB ID: retro_hsap_1539

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:25154078..25154972(-)
• Located in intron of: ENSG00000128739

Retrocopy information

• Ensembl ID: ENSG00000241061
• 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_1539
ATGGGGTTTGTTAAAGTTGTTAAGAATAAGGCCTACTTTAAGAGATACCAAGTGAAATTTAGAAGACGATGATGAGAGGG
TAAAACTGATTACGATACTCGGAAACGCTTGGTGATACAGGATAAAAATAAATACAACACACTCAAATACAGGATGATAG
TTCGTGTAACAAACAGAGATATCATTTGTCAGATTGCTTATGCCCATATAGAGGGGGATATGATAGTCTGCACAGCATAT
GCACACGAACTGCCAAAATATGGTGTGAAGGTTGGCCCGACAAATTATGCTGCAGCATATTGTACTGGCCTGCCGCTGGC
CCGCAGGCTTCTCAGTAGGTTTGGCATGGACAAGATCTATGAAGGCCAAGTGGAGGTGACTGGCGATGAATACATTGTGG
AAAGCATTGATGGTCAGCCAAGTGCCTTTACCTGCTATTTGGATGCAGGCCTTGCCAGAACTACCACTGGCAATAAAGTT
TTTGGTGCCCTGAAGGGAGCTGTGGATGGAGGCTTGTCTATCCCTCACAGTACCAAACAATTCCCTGGTTATGGTTCTGA
AAGCAAGGAATTTAATGCAGAAGTACACCGGAAGCACATCATGGGCCAGAATGTTGCCGATTACATGTGCTACTTAATGG
AAGAAGATGAAAATGCTTACAAGAAACAGTTCTCTCAATACATAAAGAACAGGGTAACTCCAGACATGATGGAGGAAATG
TATAAGGAAGCTCATGCTGCTATACGAGAGAATCCAGTCTATGAAAATAAGCCCAAGAAAGAAGTTAAAAAGAAGAGGTG
GAACCATCCCAAAATGTCCCTTGCTCAGAAGAAGGATTGGGTAGCTCAAAAGAATGCAAGCTTCCTCAGAGCTCAGAAGC
AGGCTGCTGAGAGC

Alignment

ORF - retro_hsap_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFVKVVKNKAYFKRYQVKFRRRR-EGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARI
          MGFVKVVKNKAYFKRYQVKFRRR..EGKTDY..RKRLVIQDKNKYNT.KYRMIVRVTNRDIICQIAYA.I
Retrocopy MGFVKVVKNKAYFKRYQVKFRRR**EGKTDYDTRKRLVIQDKNKYNTLKYRMIVRVTNRDIICQIAYAHI

Parental  EGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQP
          EGDMIVC.AYAHELPKYGVKVG.TNYAAAYCTGL.LARRLL.RFGMDKIYEGQVEVTGDEY.VESIDGQP
Retrocopy EGDMIVCTAYAHELPKYGVKVGPTNYAAAYCTGLPLARRLLSRFGMDKIYEGQVEVTGDEYIVESIDGQP

Parental  GAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR
          .AFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTK.FPGY.SESKEFNAEVHRKHIMGQNVADYM.
Retrocopy SAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKQFPGYGSESKEFNAEVHRKHIMGQNVADYMC

Parental  YLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDR
          YLMEEDE.AYKKQFSQYIKN.VTPDMMEEMYK.AHAAIRENPVYE.KPKKEVKKKRWN.PKMSLAQKKD.
Retrocopy YLMEEDENAYKKQFSQYIKNRVTPDMMEEMYKEAHAAIRENPVYENKPKKEVKKKRWNHPKMSLAQKKDW

Parental  VAQKKASFLRAQERAAES
          VAQK.ASFLRAQ..AAES
Retrocopy VAQKNASFLRAQKQAAES

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	0.08 RPM	831.47 RPM
bodymap2_adrenal	0.04 RPM	1088.69 RPM
bodymap2_brain	0.14 RPM	287.02 RPM
bodymap2_breast	0.08 RPM	690.73 RPM
bodymap2_colon	0.04 RPM	1255.57 RPM
bodymap2_heart	0.13 RPM	286.90 RPM
bodymap2_kidney	0.02 RPM	467.21 RPM
bodymap2_liver	0.02 RPM	264.66 RPM
bodymap2_lung	0.00 RPM	964.12 RPM
bodymap2_lymph_node	0.02 RPM	1025.32 RPM
bodymap2_ovary	0.13 RPM	2109.24 RPM
bodymap2_prostate	3.22 RPM	1546.91 RPM
bodymap2_skeletal_muscle	0.05 RPM	345.73 RPM
bodymap2_testis	0.21 RPM	860.64 RPM
bodymap2_thyroid	0.06 RPM	950.21 RPM
bodymap2_white_blood_cells	0.06 RPM	1265.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1539 was not detected

EST

No EST(s) were mapped for retro_hsap_1539 retrocopy.

TSS

No TSS is located nearby retro_hsap_1539 retrocopy 5' end.

Lab

retro_hsap_1539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1539 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1038

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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	0.32 RPM
CEU_NA11843	0.34 RPM
CEU_NA11930	0.78 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.25 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.36 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.27 RPM
CEU_NA12873	0.16 RPM
FIN_HG00183	0.41 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.41 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.32 RPM
FIN_HG00349	0.48 RPM
FIN_HG00375	0.17 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.28 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.23 RPM
GBR_HG00133	0.17 RPM
GBR_HG00134	0.24 RPM
GBR_HG00137	0.16 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.19 RPM
TSI_NA20512	0.25 RPM
TSI_NA20513	0.29 RPM
TSI_NA20518	0.33 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.26 RPM
TSI_NA20765	0.19 RPM
TSI_NA20771	0.45 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.20 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.15 RPM
YRI_NA19093	0.18 RPM
YRI_NA19099	0.19 RPM
YRI_NA19114	0.34 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	2.18 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.10 RPM

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Indel association:

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