RetrogeneDB ID: retro_hsap_2544

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:19779816..19780614(+)
• Located in intron of: ENSG00000185838

Retrocopy information

• Ensembl ID: ENSG00000235776
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL7A
• Ensembl ID: ENSG00000148303
• Aliases: RPL7A, L7A, SURF3, TRUP
• Description: ribosomal protein L7a [Source:HGNC Symbol;Acc:10364]

Sequence

>retro_hsap_2544
ATGCCAAAAGGAAAGAAGGCCAAGGGAAAGAAGGTGGCTCTGGCCCCTGCTGTCATGAAGAAGCAGGAGGCTAAGAAAGT
GGTGAATCCCCTGTTTGAGAAAAGGCCTAAGAATTTTGGCATCGGACAGGACATCCAGCCCAAAAGAGACCTCACCCACT
TTGTGAAATGGCCCCGCTATATCAGGTTGCAGCGGCAGAGAGCCATCCTCTATAAGCGGCTGAAAGTGCCTCCTGCAATT
AACCAGTTCACCTAGGCCCTGGACTGCCAAACAGCTACTCAGCTGCTTAAGCTGGCCCACAAGTACAGACCAGAGACAAA
GCAAGAGAAGAAGCAGAGACTGTTGGCCTGGGCTGAGAAGAAAGCTGCTGGCAAACGGGACGTCCCCACCAAGAGACCAC
CTGTCCTTCGAGCAGGAGTTAACATCGTCACCACCTTGGTGGAGAACAAGAAAGCTCAGCTGGTGGTGATTGCAGACGAC
GTGGATCCCATCGAGCTGGTTGTCTTCTTGCCTGCCTTGTGTCGTAAAATGGGGGTCCCTTACTGCATTATCAAGGGGAA
GGCAAGACTGGGACGTCTAGTCCACAGGAAGACCTGCACCACTGTCACCTTCACATAGGTGAACTCGGAAGACAAAGGCA
CTTTGGCTAAGCTGATGGAAGCTATCAGGACCAATTACAATGACAGATACGATGAGATCCGCCGTCACTGGGGCGGCAAC
ATCCTGGGTCCTAAGTCTGTGGCTCGTATCGCCAAGCTCGAAAAGGCAAAGGCTAAAGAACTTGCCACTAAACTGGGT

Alignment

ORF - retro_hsap_2544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKGKKAKGKKVAPAPAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAIL
          MPKGKKAKGKKVA.APAV.KKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLT.FVKWPRYIRLQRQRAIL
Retrocopy MPKGKKAKGKKVALAPAVMKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTHFVKWPRYIRLQRQRAIL

Parental  YKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGV
          YKRLKVPPAINQFT.ALD.QTATQLLKLAHKYRPETKQEKKQRLLA.AEKKAAGK.DVPTKRPPVLRAGV
Retrocopy YKRLKVPPAINQFT*ALDCQTATQLLKLAHKYRPETKQEKKQRLLAWAEKKAAGKRDVPTKRPPVLRAGV

Parental  NTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSE
          N.VTTLVENKKAQLVVIA.DVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTV.FT.VNSE
Retrocopy NIVTTLVENKKAQLVVIADDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVTFT*VNSE

Parental  DKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG
          DKG.LAKL.EAIRTNYNDRYDEIRRHWGGN.LGPKSVARIAKLEKAKAKELATKLG
Retrocopy DKGTLAKLMEAIRTNYNDRYDEIRRHWGGNILGPKSVARIAKLEKAKAKELATKLG

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	0.18 RPM	630.89 RPM
bodymap2_adrenal	0.51 RPM	818.53 RPM
bodymap2_brain	0.14 RPM	138.06 RPM
bodymap2_breast	0.31 RPM	428.06 RPM
bodymap2_colon	0.29 RPM	800.16 RPM
bodymap2_heart	0.06 RPM	174.83 RPM
bodymap2_kidney	0.14 RPM	375.99 RPM
bodymap2_liver	0.08 RPM	230.18 RPM
bodymap2_lung	0.09 RPM	639.05 RPM
bodymap2_lymph_node	0.00 RPM	731.09 RPM
bodymap2_ovary	0.21 RPM	1017.07 RPM
bodymap2_prostate	0.14 RPM	927.73 RPM
bodymap2_skeletal_muscle	0.16 RPM	405.24 RPM
bodymap2_testis	0.09 RPM	481.94 RPM
bodymap2_thyroid	0.08 RPM	506.97 RPM
bodymap2_white_blood_cells	0.10 RPM	875.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2544 was not detected

EST

No EST(s) were mapped for retro_hsap_2544 retrocopy.

TSS

No TSS is located nearby retro_hsap_2544 retrocopy 5' end.

Lab

retro_hsap_2544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2544 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1591
Pongo abelii	retro_pabe_1871

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 289 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011708	29 retrocopies	retro_amel_1000, retro_amel_1058, retro_amel_1149, retro_amel_1159, retro_amel_1207, retro_amel_1220, retro_amel_1269, retro_amel_1314, retro_amel_1417, retro_amel_142, retro_amel_1429, retro_amel_1471, retro_amel_1499, retro_amel_1506, retro_amel_1641, retro_amel_1644, retro_amel_169, retro_amel_170, retro_amel_1812, retro_amel_1873, retro_amel_357, retro_amel_463, retro_amel_525, retro_amel_529, retro_amel_544, retro_amel_671, retro_amel_726, retro_amel_758, retro_amel_801,
Bos taurus	ENSBTAG00000011559	5 retrocopies	retro_btau_1345, retro_btau_1494, retro_btau_564, retro_btau_890, retro_btau_936,
Canis familiaris	ENSCAFG00000017680	36 retrocopies	retro_cfam_1121, retro_cfam_1123, retro_cfam_1165, retro_cfam_1187, retro_cfam_1242, retro_cfam_1365, retro_cfam_1429, retro_cfam_1471, retro_cfam_1497, retro_cfam_1532, retro_cfam_1553, retro_cfam_1563, retro_cfam_1683, retro_cfam_1711, retro_cfam_1721, retro_cfam_1750, retro_cfam_1865, retro_cfam_1898, retro_cfam_2032, retro_cfam_2103, retro_cfam_2111, retro_cfam_2120, retro_cfam_2144, retro_cfam_311, retro_cfam_340, retro_cfam_380, retro_cfam_423, retro_cfam_476, retro_cfam_518, retro_cfam_605, retro_cfam_694, retro_cfam_723, retro_cfam_827, retro_cfam_853, retro_cfam_927, retro_cfam_935,
Callithrix jacchus	ENSCJAG00000014827	3 retrocopies	retro_cjac_199, retro_cjac_343, retro_cjac_49,
Dipodomys ordii	ENSDORG00000006471	3 retrocopies	retro_dord_198, retro_dord_218, retro_dord_516,
Equus caballus	ENSECAG00000008548	2 retrocopies	retro_ecab_4, retro_ecab_402,
Felis catus	ENSFCAG00000005825	20 retrocopies	retro_fcat_1123, retro_fcat_1137, retro_fcat_1170, retro_fcat_1277, retro_fcat_1315, retro_fcat_1318, retro_fcat_1344, retro_fcat_1528, retro_fcat_1583, retro_fcat_1771, retro_fcat_1980, retro_fcat_214, retro_fcat_252, retro_fcat_385, retro_fcat_389, retro_fcat_468, retro_fcat_542, retro_fcat_628, retro_fcat_694, retro_fcat_943,
Homo sapiens	ENSG00000148303	21 retrocopies	retro_hsap_1229, retro_hsap_1438, retro_hsap_2037, retro_hsap_2544 , retro_hsap_3019, retro_hsap_3081, retro_hsap_3133, retro_hsap_3202, retro_hsap_3421, retro_hsap_3503, retro_hsap_3668, retro_hsap_3830, retro_hsap_3890, retro_hsap_428, retro_hsap_4296, retro_hsap_467, retro_hsap_4754, retro_hsap_682, retro_hsap_707, retro_hsap_801, retro_hsap_809,
Gorilla gorilla	ENSGGOG00000014442	48 retrocopies	retro_ggor_1034, retro_ggor_1042, retro_ggor_1087, retro_ggor_1107, retro_ggor_1190, retro_ggor_1249, retro_ggor_1408, retro_ggor_1409, retro_ggor_1460, retro_ggor_1541, retro_ggor_1591, retro_ggor_172, retro_ggor_1724, retro_ggor_1881, retro_ggor_194, retro_ggor_2004, retro_ggor_2033, retro_ggor_2087, retro_ggor_2117, retro_ggor_2147, retro_ggor_2313, retro_ggor_2410, retro_ggor_2430, retro_ggor_2480, retro_ggor_2522, retro_ggor_2578, retro_ggor_2611, retro_ggor_2617, retro_ggor_2618, retro_ggor_2779, retro_ggor_2781, retro_ggor_2871, retro_ggor_2872, retro_ggor_288, retro_ggor_2960, retro_ggor_310, retro_ggor_333, retro_ggor_386, retro_ggor_539, retro_ggor_626, retro_ggor_636, retro_ggor_640, retro_ggor_658, retro_ggor_663, retro_ggor_815, retro_ggor_865, retro_ggor_904, retro_ggor_963,
Loxodonta africana	ENSLAFG00000006436	2 retrocopies	retro_lafr_1059, retro_lafr_1132,
Macropus eugenii	ENSMEUG00000014550	16 retrocopies	retro_meug_1268, retro_meug_133, retro_meug_1362, retro_meug_1523, retro_meug_1581, retro_meug_1872, retro_meug_2011, retro_meug_2080, retro_meug_2101, retro_meug_2123, retro_meug_401, retro_meug_632, retro_meug_654, retro_meug_687, retro_meug_699, retro_meug_919,
Macaca mulatta	ENSMMUG00000022341	9 retrocopies	retro_mmul_113, retro_mmul_130, retro_mmul_204, retro_mmul_230, retro_mmul_252, retro_mmul_259, retro_mmul_309, retro_mmul_33, retro_mmul_4,
Monodelphis domestica	ENSMODG00000012754	3 retrocopies	retro_mdom_1347, retro_mdom_418, retro_mdom_586,
Mustela putorius furo	ENSMPUG00000012398	13 retrocopies	retro_mputfur_1081, retro_mputfur_1210, retro_mputfur_1281, retro_mputfur_1344, retro_mputfur_1380, retro_mputfur_1611, retro_mputfur_1612, retro_mputfur_325, retro_mputfur_459, retro_mputfur_656, retro_mputfur_698, retro_mputfur_792, retro_mputfur_900,
Mus musculus	ENSMUSG00000062647	10 retrocopies	retro_mmus_120, retro_mmus_141, retro_mmus_165, retro_mmus_166, retro_mmus_214, retro_mmus_226, retro_mmus_267, retro_mmus_34, retro_mmus_43, retro_mmus_93,
Nomascus leucogenys	ENSNLEG00000013068	22 retrocopies	retro_nleu_1051, retro_nleu_1056, retro_nleu_137, retro_nleu_1404, retro_nleu_1418, retro_nleu_1682, retro_nleu_1920, retro_nleu_2130, retro_nleu_2254, retro_nleu_2341, retro_nleu_2397, retro_nleu_2423, retro_nleu_2641, retro_nleu_267, retro_nleu_2822, retro_nleu_2853, retro_nleu_399, retro_nleu_432, retro_nleu_562, retro_nleu_780, retro_nleu_796, retro_nleu_82,
Otolemur garnettii	ENSOGAG00000014027	16 retrocopies	retro_ogar_1014, retro_ogar_1172, retro_ogar_1638, retro_ogar_1735, retro_ogar_1815, retro_ogar_2774, retro_ogar_3012, retro_ogar_3097, retro_ogar_319, retro_ogar_404, retro_ogar_57, retro_ogar_685, retro_ogar_758, retro_ogar_850, retro_ogar_926, retro_ogar_994,
Pteropus vampyrus	ENSPVAG00000017045	11 retrocopies	retro_pvam_1240, retro_pvam_125, retro_pvam_1288, retro_pvam_1371, retro_pvam_1472, retro_pvam_270, retro_pvam_307, retro_pvam_333, retro_pvam_510, retro_pvam_540, retro_pvam_640,
Rattus norvegicus	ENSRNOG00000049097	10 retrocopies	retro_rnor_123, retro_rnor_15, retro_rnor_238, retro_rnor_303, retro_rnor_323, retro_rnor_346, retro_rnor_368, retro_rnor_398, retro_rnor_403, retro_rnor_86,
Sarcophilus harrisii	ENSSHAG00000004337	4 retrocopies	retro_shar_157, retro_shar_338, retro_shar_401, retro_shar_494,
Ictidomys tridecemlineatus	ENSSTOG00000003671	3 retrocopies	retro_itri_1034, retro_itri_53, retro_itri_920,
Tursiops truncatus	ENSTTRG00000007645	3 retrocopies	retro_ttru_1334, retro_ttru_1681, retro_ttru_1824,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.28 RPM
CEU_NA11843	0.40 RPM
CEU_NA11930	0.68 RPM
CEU_NA12004	0.27 RPM
CEU_NA12400	0.42 RPM
CEU_NA12751	0.24 RPM
CEU_NA12760	0.63 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.41 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.27 RPM
FIN_HG00328	0.26 RPM
FIN_HG00338	0.28 RPM
FIN_HG00349	0.31 RPM
FIN_HG00375	0.44 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.19 RPM
GBR_HG00099	0.26 RPM
GBR_HG00111	0.39 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.19 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.47 RPM
GBR_HG00142	0.25 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.42 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.78 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.35 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.28 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.41 RPM
YRI_NA18907	0.21 RPM
YRI_NA18916	0.17 RPM
YRI_NA19093	0.16 RPM
YRI_NA19099	0.27 RPM
YRI_NA19114	0.21 RPM
YRI_NA19118	0.23 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.25 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).