RetrogeneDB ID: retro_hsap_2497

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:20230096..20230591(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000198618
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIA
• Ensembl ID: ENSG00000196262
• Aliases: PPIA, CYPA, CYPH, HEL-S-69p
• Description: peptidylprolyl isomerase A (cyclophilin A) [Source:HGNC Symbol;Acc:9253]

Sequence

>retro_hsap_2497
ATGGTCAACCCCACCGTGTTCTTCGACATTGCCGTCGACGGCGAGCCCTTGGGCCGCGTCTCCTTTGAGCTGTTTGCAGA
CAAGGTCCCAAAGACAGCAGAAAATTTTCGTGCTCTGAGCACTGGAGAGAAAGGATTTGGTTATAAGGGTTCCTGCTTTC
ACAGAATTATTCCAGGGTTTATGTGTCAGGGTGGTGACTTCACACGCCATAATGGCACTGGTGGCAAGTCCATCTATGGG
GAGAAATTTGAAGATGAGAACTTCATCCTAAAGCATACAGGTCCTGGCATCTTGTCCATGGCAAATGCTGGACCCAACAC
AAATGGATCCCAGTTTTTCATCTGCACTGCCAAGACTGAGTGGTTGGATGGCAAGCATGTGGTGTTTGGCAAAGTGAAAG
AAGGCATGAATATTGTGGAGGCCATGGAGCGCTTTGGGTCCAGGAATGGCAAGACCAGCAAGAAGATCACCATTGCTGAC
TGTGGACAACTCGAA

Alignment

ORF - retro_hsap_2497 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRH
          MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRH
Retrocopy MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRH

Parental  NGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVE
          NGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVE
Retrocopy NGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVE

Parental  AMERFGSRNGKTSKKITIADCGQLE
          AMERFGSRNGKTSKKITIADCGQLE
Retrocopy AMERFGSRNGKTSKKITIADCGQLE

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	1.73 RPM	74.14 RPM
bodymap2_adrenal	3.42 RPM	190.55 RPM
bodymap2_brain	2.86 RPM	151.99 RPM
bodymap2_breast	1.83 RPM	103.76 RPM
bodymap2_colon	1.82 RPM	100.26 RPM
bodymap2_heart	3.84 RPM	59.61 RPM
bodymap2_kidney	4.82 RPM	183.79 RPM
bodymap2_liver	7.79 RPM	129.95 RPM
bodymap2_lung	14.72 RPM	194.15 RPM
bodymap2_lymph_node	13.61 RPM	179.98 RPM
bodymap2_ovary	1.48 RPM	92.74 RPM
bodymap2_prostate	10.58 RPM	165.42 RPM
bodymap2_skeletal_muscle	6.24 RPM	77.57 RPM
bodymap2_testis	1.40 RPM	81.18 RPM
bodymap2_thyroid	2.07 RPM	98.32 RPM
bodymap2_white_blood_cells	10.32 RPM	209.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2497 was not detected

EST

No EST(s) were mapped for retro_hsap_2497 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_104068	839 libraries	772 libraries	213 libraries	4 libraries	1 library

The graphical summary, for retro_hsap_2497 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_2497 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2497 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1449

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 376 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012003	12 retrocopies	retro_btau_1005, retro_btau_1448, retro_btau_155, retro_btau_1696, retro_btau_1806, retro_btau_272, retro_btau_334, retro_btau_335, retro_btau_345, retro_btau_414, retro_btau_751, retro_btau_934,
Callithrix jacchus	ENSCJAG00000011969	54 retrocopies	retro_cjac_1065, retro_cjac_1080, retro_cjac_1083, retro_cjac_1092, retro_cjac_1097, retro_cjac_11, retro_cjac_1193, retro_cjac_1213, retro_cjac_1310, retro_cjac_1326, retro_cjac_1347, retro_cjac_1451, retro_cjac_147, retro_cjac_1678, retro_cjac_1710, retro_cjac_1760, retro_cjac_1782, retro_cjac_1982, retro_cjac_1989, retro_cjac_2043, retro_cjac_2060, retro_cjac_2062, retro_cjac_2118, retro_cjac_2286, retro_cjac_2327, retro_cjac_2376, retro_cjac_2425, retro_cjac_2426, retro_cjac_2479, retro_cjac_2540, retro_cjac_2688, retro_cjac_2863, retro_cjac_2881, retro_cjac_2977, retro_cjac_3073, retro_cjac_3077, retro_cjac_3101, retro_cjac_3196, retro_cjac_384, retro_cjac_4202, retro_cjac_4203, retro_cjac_501, retro_cjac_646, retro_cjac_649, retro_cjac_695, retro_cjac_704, retro_cjac_710, retro_cjac_714, retro_cjac_717, retro_cjac_755, retro_cjac_827, retro_cjac_834, retro_cjac_871, retro_cjac_971,
Echinops telfairi	ENSETEG00000002186	21 retrocopies	retro_etel_115, retro_etel_1188, retro_etel_1292, retro_etel_1322, retro_etel_1670, retro_etel_1827, retro_etel_1875, retro_etel_1886, retro_etel_208, retro_etel_25, retro_etel_288, retro_etel_371, retro_etel_430, retro_etel_447, retro_etel_485, retro_etel_537, retro_etel_551, retro_etel_568, retro_etel_595, retro_etel_937, retro_etel_998,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Homo sapiens	ENSG00000196262	78 retrocopies	retro_hsap_1149, retro_hsap_1196, retro_hsap_1206, retro_hsap_1239, retro_hsap_1286, retro_hsap_1297, retro_hsap_1326, retro_hsap_1346, retro_hsap_1515, retro_hsap_1645, retro_hsap_1651, retro_hsap_1653, retro_hsap_1709, retro_hsap_1753, retro_hsap_1779, retro_hsap_1872, retro_hsap_1991, retro_hsap_2065, retro_hsap_2077, retro_hsap_2081, retro_hsap_2105, retro_hsap_2154, retro_hsap_2203, retro_hsap_2255, retro_hsap_2297, retro_hsap_2345, retro_hsap_242, retro_hsap_2426, retro_hsap_2429, retro_hsap_2464, retro_hsap_2497 , retro_hsap_2518, retro_hsap_2641, retro_hsap_2652, retro_hsap_2717, retro_hsap_2727, retro_hsap_2788, retro_hsap_2789, retro_hsap_2792, retro_hsap_2794, retro_hsap_2826, retro_hsap_2843, retro_hsap_2886, retro_hsap_2978, retro_hsap_3184, retro_hsap_3310, retro_hsap_3348, retro_hsap_3351, retro_hsap_354, retro_hsap_3575, retro_hsap_375, retro_hsap_3751, retro_hsap_3781, retro_hsap_3835, retro_hsap_3880, retro_hsap_3916, retro_hsap_3960, retro_hsap_3966, retro_hsap_4035, retro_hsap_4128, retro_hsap_4274, retro_hsap_4285, retro_hsap_429, retro_hsap_4298, retro_hsap_4773, retro_hsap_4882, retro_hsap_527, retro_hsap_630, retro_hsap_649, retro_hsap_657, retro_hsap_694, retro_hsap_728, retro_hsap_733, retro_hsap_741, retro_hsap_774, retro_hsap_816, retro_hsap_839, retro_hsap_876,
Gorilla gorilla	ENSGGOG00000026298	4 retrocopies	retro_ggor_138, retro_ggor_15, retro_ggor_165, retro_ggor_28,
Macropus eugenii	ENSMEUG00000002016	20 retrocopies	retro_meug_1024, retro_meug_1055, retro_meug_1089, retro_meug_1133, retro_meug_1269, retro_meug_1391, retro_meug_1576, retro_meug_1746, retro_meug_1880, retro_meug_1975, retro_meug_2013, retro_meug_2037, retro_meug_260, retro_meug_297, retro_meug_301, retro_meug_437, retro_meug_478, retro_meug_510, retro_meug_713, retro_meug_73,
Macaca mulatta	ENSMMUG00000016638	10 retrocopies	retro_mmul_1, retro_mmul_13, retro_mmul_132, retro_mmul_141, retro_mmul_161, retro_mmul_195, retro_mmul_245, retro_mmul_5, retro_mmul_56, retro_mmul_8,
Monodelphis domestica	ENSMODG00000016089	9 retrocopies	retro_mdom_1373, retro_mdom_1524, retro_mdom_1856, retro_mdom_1884, retro_mdom_215, retro_mdom_272, retro_mdom_29, retro_mdom_730, retro_mdom_85,
Mus musculus	ENSMUSG00000071866	2 retrocopies	retro_mmus_242, retro_mmus_285,
Oryctolagus cuniculus	ENSOCUG00000016662	3 retrocopies	retro_ocun_113, retro_ocun_1406, retro_ocun_237,
Otolemur garnettii	ENSOGAG00000027997	31 retrocopies	retro_ogar_1090, retro_ogar_1201, retro_ogar_1305, retro_ogar_1329, retro_ogar_1336, retro_ogar_1562, retro_ogar_1634, retro_ogar_1741, retro_ogar_1889, retro_ogar_1893, retro_ogar_1920, retro_ogar_1973, retro_ogar_1974, retro_ogar_1999, retro_ogar_21, retro_ogar_2246, retro_ogar_2265, retro_ogar_2397, retro_ogar_2401, retro_ogar_2440, retro_ogar_2484, retro_ogar_2794, retro_ogar_2907, retro_ogar_2924, retro_ogar_2938, retro_ogar_2948, retro_ogar_3072, retro_ogar_3187, retro_ogar_3210, retro_ogar_357, retro_ogar_743,
Pongo abelii	ENSPPYG00000017586	12 retrocopies	retro_pabe_1065, retro_pabe_1330, retro_pabe_186, retro_pabe_221, retro_pabe_2267, retro_pabe_2469, retro_pabe_2633, retro_pabe_2730, retro_pabe_2812, retro_pabe_3474, retro_pabe_631, retro_pabe_995,
Pongo abelii	ENSPPYG00000017587	4 retrocopies	retro_pabe_1118, retro_pabe_2202, retro_pabe_3311, retro_pabe_3602,
Rattus norvegicus	ENSRNOG00000006423	2 retrocopies	retro_rnor_360, retro_rnor_387,
Sarcophilus harrisii	ENSSHAG00000017062	3 retrocopies	retro_shar_164, retro_shar_383, retro_shar_750,
Ictidomys tridecemlineatus	ENSSTOG00000010215	10 retrocopies	retro_itri_1073, retro_itri_1576, retro_itri_1683, retro_itri_1897, retro_itri_499, retro_itri_667, retro_itri_7, retro_itri_731, retro_itri_802, retro_itri_978,
Tupaia belangeri	ENSTBEG00000017484	77 retrocopies	retro_tbel_1014, retro_tbel_1098, retro_tbel_1104, retro_tbel_1106, retro_tbel_1180, retro_tbel_1661, retro_tbel_1689, retro_tbel_1808, retro_tbel_1813, retro_tbel_1831, retro_tbel_1895, retro_tbel_1904, retro_tbel_1913, retro_tbel_1918, retro_tbel_1936, retro_tbel_1938, retro_tbel_2013, retro_tbel_2014, retro_tbel_204, retro_tbel_2054, retro_tbel_2098, retro_tbel_2144, retro_tbel_2175, retro_tbel_221, retro_tbel_2557, retro_tbel_267, retro_tbel_2681, retro_tbel_2691, retro_tbel_2714, retro_tbel_2824, retro_tbel_2834, retro_tbel_2851, retro_tbel_2897, retro_tbel_2938, retro_tbel_3004, retro_tbel_3054, retro_tbel_3104, retro_tbel_3142, retro_tbel_3153, retro_tbel_3311, retro_tbel_3337, retro_tbel_3421, retro_tbel_3423, retro_tbel_3477, retro_tbel_3639, retro_tbel_3691, retro_tbel_3767, retro_tbel_3847, retro_tbel_3880, retro_tbel_3890, retro_tbel_3979, retro_tbel_4019, retro_tbel_415, retro_tbel_4155, retro_tbel_4325, retro_tbel_4332, retro_tbel_4364, retro_tbel_4391, retro_tbel_4534, retro_tbel_4537, retro_tbel_4568, retro_tbel_4581, retro_tbel_4683, retro_tbel_4699, retro_tbel_521, retro_tbel_541, retro_tbel_618, retro_tbel_64, retro_tbel_764, retro_tbel_80, retro_tbel_831, retro_tbel_832, retro_tbel_887, retro_tbel_900, retro_tbel_910, retro_tbel_922, retro_tbel_946,
Tarsius syrichta	ENSTSYG00000008973	23 retrocopies	retro_tsyr_1106, retro_tsyr_1266, retro_tsyr_1277, retro_tsyr_1530, retro_tsyr_1643, retro_tsyr_1816, retro_tsyr_1909, retro_tsyr_2040, retro_tsyr_2072, retro_tsyr_2097, retro_tsyr_388, retro_tsyr_400, retro_tsyr_408, retro_tsyr_430, retro_tsyr_459, retro_tsyr_478, retro_tsyr_481, retro_tsyr_507, retro_tsyr_641, retro_tsyr_705, retro_tsyr_760, retro_tsyr_847, retro_tsyr_924,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	12.48 RPM
CEU_NA11843	11.60 RPM
CEU_NA11930	11.08 RPM
CEU_NA12004	11.89 RPM
CEU_NA12400	15.36 RPM
CEU_NA12751	11.41 RPM
CEU_NA12760	15.99 RPM
CEU_NA12827	14.43 RPM
CEU_NA12872	10.51 RPM
CEU_NA12873	12.95 RPM
FIN_HG00183	12.16 RPM
FIN_HG00277	9.35 RPM
FIN_HG00315	16.59 RPM
FIN_HG00321	9.07 RPM
FIN_HG00328	12.24 RPM
FIN_HG00338	17.03 RPM
FIN_HG00349	12.06 RPM
FIN_HG00375	11.54 RPM
FIN_HG00377	14.67 RPM
FIN_HG00378	13.41 RPM
GBR_HG00099	12.90 RPM
GBR_HG00111	15.60 RPM
GBR_HG00114	12.41 RPM
GBR_HG00119	9.15 RPM
GBR_HG00131	9.66 RPM
GBR_HG00133	10.06 RPM
GBR_HG00134	13.56 RPM
GBR_HG00137	11.49 RPM
GBR_HG00142	6.64 RPM
GBR_HG00143	13.08 RPM
TSI_NA20512	22.83 RPM
TSI_NA20513	9.00 RPM
TSI_NA20518	13.82 RPM
TSI_NA20532	13.20 RPM
TSI_NA20538	8.25 RPM
TSI_NA20756	13.88 RPM
TSI_NA20765	13.84 RPM
TSI_NA20771	10.41 RPM
TSI_NA20786	11.59 RPM
TSI_NA20798	15.34 RPM
YRI_NA18870	16.18 RPM
YRI_NA18907	13.76 RPM
YRI_NA18916	15.14 RPM
YRI_NA19093	13.85 RPM
YRI_NA19099	16.32 RPM
YRI_NA19114	14.42 RPM
YRI_NA19118	13.05 RPM
YRI_NA19213	8.04 RPM
YRI_NA19214	13.13 RPM
YRI_NA19223	12.85 RPM

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Indel association:

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