RetrogeneDB ID: retro_btau_1669

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:24048704..24049227(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000034315
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPSA
• Ensembl ID: ENSBTAG00000009757
• Aliases: RPSA, LAMR1
• Description: 40S ribosomal protein SA [Source:UniProtKB/Swiss-Prot;Acc:P26452]

Sequence

>retro_btau_1669
ATGTCCAAAATCCTTGATGTGATGCAAATGAAGGAGAAGGATGTCCTCAAATTTCTTGCTGCAGGAACCCACTTAGGTGG
CCCCAACCTTGACTTCCAGATGGAATGGCACATCTGCCAAAGGAAAGCTCATGGCATGTACATCATAAGTATGAAGAGAA
CCTGAGAGAAACTTCTGTTGGCAGCGTGTCAGAGGTGCCATTGAAAACCCAACTGATGTCAGTTTCACATTCTCCAGGAA
TACCGGCCATTCAGTTGTGCTGGAGTCCGGGGCTGCCACTGGAGGCACTCCTATTGCTGGCCGCTTTACTTCTGGAAACT
TCACTAACCAGATTCAGGCAGCCTTCCAGGGGCCAAGACTTCTGGTGGTTACTGATCCCAGGGCTGACCACTGGCCTCTT
ACAGAAGCCTCATATATTAACTCGTTTAGCATTGCTCTATGTAACACAGACTCTCCCCTGTGCTGTGTGGACATCACCAT
TCTGTGCAACAAGGGAGCTCACTCAGTGGGTCTGATGTAGTGG

Alignment

ORF - retro_btau_1669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA-RAIVAIE
          MS..LDV.QMKE.DVLKFLAAGTHLGG.NLDFQME..I..RK..G.YII..KRT.EK.LL.A.R...AIE
Retrocopy MSKILDVMQMKEKDVLKFLAAGTHLGGPNLDFQMEWHICQRKAHGMYIISMKRT*EK-LLLA>RVRGAIE

Parental  NPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASY
          NP.DVS...SRNTG...VL...AATG.TPIAGRFT.G.FTNQIQAAF..PRLLVVTDPRADH.PLTEASY
Retrocopy NPTDVSFTFSRNTGHSVVLESGAATGGTPIAGRFTSGNFTNQIQAAFQGPRLLVVTDPRADHWPLTEASY

Parental  VNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWW
          .N...IALCNTDSPL..VDI.I.C.NKGAHSVGLM.W
Retrocopy INSFSIALCNTDSPLCCVDITILC-NKGAHSVGLM*W

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
ERP005899_liver	0.00 RPM	238.78 RPM
ERP005899_muscle	0.00 RPM	2624.41 RPM
SRP017611_brain	0.00 RPM	143.57 RPM
SRP017611_kidney	0.00 RPM	562.13 RPM
SRP017611_liver	0.00 RPM	395.29 RPM
SRP030211_testis	0.01 RPM	299.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1669 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1669 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 305 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004183	1 retrocopy	retro_acar_140,
Ailuropoda melanoleuca	ENSAMEG00000008962	13 retrocopies	retro_amel_1091, retro_amel_1276, retro_amel_1357, retro_amel_1432, retro_amel_1446, retro_amel_1497, retro_amel_1634, retro_amel_1817, retro_amel_1857, retro_amel_196, retro_amel_430, retro_amel_808, retro_amel_943,
Bos taurus	ENSBTAG00000009757	19 retrocopies	retro_btau_1037, retro_btau_1063, retro_btau_1091, retro_btau_1107, retro_btau_1158, retro_btau_1234, retro_btau_1288, retro_btau_1580, retro_btau_1633, retro_btau_1669 , retro_btau_1716, retro_btau_1756, retro_btau_1770, retro_btau_416, retro_btau_848, retro_btau_871, retro_btau_896, retro_btau_964, retro_btau_990,
Canis familiaris	ENSCAFG00000005101	27 retrocopies	retro_cfam_1046, retro_cfam_1109, retro_cfam_1173, retro_cfam_1189, retro_cfam_1263, retro_cfam_1288, retro_cfam_1366, retro_cfam_1373, retro_cfam_1435, retro_cfam_1511, retro_cfam_1534, retro_cfam_1545, retro_cfam_1555, retro_cfam_1679, retro_cfam_1770, retro_cfam_1814, retro_cfam_1957, retro_cfam_1990, retro_cfam_2140, retro_cfam_512, retro_cfam_820, retro_cfam_828, retro_cfam_854, retro_cfam_928, retro_cfam_957, retro_cfam_980, retro_cfam_994,
Callithrix jacchus	ENSCJAG00000009675	15 retrocopies	retro_cjac_1113, retro_cjac_1572, retro_cjac_1595, retro_cjac_2265, retro_cjac_2438, retro_cjac_2500, retro_cjac_2502, retro_cjac_2750, retro_cjac_2897, retro_cjac_305, retro_cjac_3160, retro_cjac_4124, retro_cjac_53, retro_cjac_732, retro_cjac_958,
Cavia porcellus	ENSCPOG00000008715	7 retrocopies	retro_cpor_1206, retro_cpor_1255, retro_cpor_1293, retro_cpor_594, retro_cpor_624, retro_cpor_806, retro_cpor_958,
Dasypus novemcinctus	ENSDNOG00000004048	27 retrocopies	retro_dnov_1022, retro_dnov_108, retro_dnov_1099, retro_dnov_1219, retro_dnov_1372, retro_dnov_1431, retro_dnov_1614, retro_dnov_184, retro_dnov_1913, retro_dnov_1974, retro_dnov_1987, retro_dnov_1988, retro_dnov_2067, retro_dnov_2200, retro_dnov_2224, retro_dnov_2309, retro_dnov_2339, retro_dnov_2469, retro_dnov_2480, retro_dnov_375, retro_dnov_42, retro_dnov_456, retro_dnov_465, retro_dnov_663, retro_dnov_800, retro_dnov_895, retro_dnov_940,
Equus caballus	ENSECAG00000013062	5 retrocopies	retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Erinaceus europaeus	ENSEEUG00000005292	2 retrocopies	retro_eeur_202, retro_eeur_679,
Echinops telfairi	ENSETEG00000018160	4 retrocopies	retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Felis catus	ENSFCAG00000002739	22 retrocopies	retro_fcat_1119, retro_fcat_1127, retro_fcat_1239, retro_fcat_1353, retro_fcat_1595, retro_fcat_1668, retro_fcat_1694, retro_fcat_1720, retro_fcat_1758, retro_fcat_1804, retro_fcat_1807, retro_fcat_1861, retro_fcat_1970, retro_fcat_239, retro_fcat_258, retro_fcat_384, retro_fcat_391, retro_fcat_551, retro_fcat_682, retro_fcat_722, retro_fcat_793, retro_fcat_906,
Homo sapiens	ENSG00000168028	2 retrocopies	retro_hsap_107, retro_hsap_3015,
Gorilla gorilla	ENSGGOG00000015038	11 retrocopies	retro_ggor_1069, retro_ggor_1095, retro_ggor_1110, retro_ggor_1277, retro_ggor_1729, retro_ggor_2325, retro_ggor_2461, retro_ggor_2671, retro_ggor_2804, retro_ggor_2811, retro_ggor_62,
Loxodonta africana	ENSLAFG00000032009	5 retrocopies	retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Macaca mulatta	ENSMMUG00000007930	2 retrocopies	retro_mmul_1789, retro_mmul_592,
Macaca mulatta	ENSMMUG00000022965	19 retrocopies	retro_mmul_1008, retro_mmul_1167, retro_mmul_120, retro_mmul_1237, retro_mmul_136, retro_mmul_1527, retro_mmul_1678, retro_mmul_1755, retro_mmul_1879, retro_mmul_1909, retro_mmul_2274, retro_mmul_2388, retro_mmul_2538, retro_mmul_2541, retro_mmul_2622, retro_mmul_378, retro_mmul_789, retro_mmul_876, retro_mmul_911,
Mustela putorius furo	ENSMPUG00000002463	21 retrocopies	retro_mputfur_1045, retro_mputfur_1143, retro_mputfur_1194, retro_mputfur_1227, retro_mputfur_1311, retro_mputfur_1318, retro_mputfur_1427, retro_mputfur_1502, retro_mputfur_1558, retro_mputfur_1584, retro_mputfur_288, retro_mputfur_358, retro_mputfur_423, retro_mputfur_477, retro_mputfur_515, retro_mputfur_560, retro_mputfur_576, retro_mputfur_712, retro_mputfur_733, retro_mputfur_932, retro_mputfur_953,
Mus musculus	ENSMUSG00000032518	1 retrocopy	retro_mmus_219,
Otolemur garnettii	ENSOGAG00000028830	8 retrocopies	retro_ogar_1507, retro_ogar_1548, retro_ogar_2094, retro_ogar_2258, retro_ogar_3126, retro_ogar_327, retro_ogar_457, retro_ogar_567,
Pongo abelii	ENSPPYG00000013993	4 retrocopies	retro_pabe_1085, retro_pabe_1142, retro_pabe_116, retro_pabe_818,
Pan troglodytes	ENSPTRG00000022841	1 retrocopy	retro_ptro_14,
Pteropus vampyrus	ENSPVAG00000007794	19 retrocopies	retro_pvam_1189, retro_pvam_1249, retro_pvam_1335, retro_pvam_1403, retro_pvam_1406, retro_pvam_1443, retro_pvam_1446, retro_pvam_396, retro_pvam_499, retro_pvam_532, retro_pvam_548, retro_pvam_60, retro_pvam_635, retro_pvam_650, retro_pvam_789, retro_pvam_889, retro_pvam_896, retro_pvam_898, retro_pvam_98,
Rattus norvegicus	ENSRNOG00000018645	27 retrocopies	retro_rnor_1004, retro_rnor_1114, retro_rnor_1119, retro_rnor_1213, retro_rnor_1301, retro_rnor_1396, retro_rnor_1481, retro_rnor_1634, retro_rnor_1778, retro_rnor_1840, retro_rnor_1886, retro_rnor_2068, retro_rnor_2153, retro_rnor_2329, retro_rnor_2384, retro_rnor_2444, retro_rnor_2553, retro_rnor_2554, retro_rnor_2589, retro_rnor_2637, retro_rnor_2649, retro_rnor_2701, retro_rnor_2810, retro_rnor_2912, retro_rnor_2958, retro_rnor_645, retro_rnor_702,
Sus scrofa	ENSSSCG00000011266	9 retrocopies	retro_sscr_1022, retro_sscr_1180, retro_sscr_22, retro_sscr_269, retro_sscr_890, retro_sscr_926, retro_sscr_966, retro_sscr_967, retro_sscr_982,
Tarsius syrichta	ENSTSYG00000004458	6 retrocopies	retro_tsyr_115, retro_tsyr_1290, retro_tsyr_156, retro_tsyr_38, retro_tsyr_456, retro_tsyr_807,
Tursiops truncatus	ENSTTRG00000014496	24 retrocopies	retro_ttru_1160, retro_ttru_1216, retro_ttru_1222, retro_ttru_1287, retro_ttru_1326, retro_ttru_1432, retro_ttru_1463, retro_ttru_148, retro_ttru_1572, retro_ttru_1693, retro_ttru_1705, retro_ttru_176, retro_ttru_1835, retro_ttru_190, retro_ttru_194, retro_ttru_303, retro_ttru_331, retro_ttru_404, retro_ttru_427, retro_ttru_477, retro_ttru_576, retro_ttru_693, retro_ttru_879, retro_ttru_967,
Vicugna pacos	ENSVPAG00000012307	4 retrocopies	retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,