RetrogeneDB ID: retro_pvam_1158

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3347:97613..98195(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSPVAG00000012882
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_pvam_1158
GGTCCCAAGATGCATCGGAAGTGTGGAGTAGCTCCAAAGCATTAGATGCTGAGTAAACTAACCAGTGTGTCTGTTCCTCA
TCCATCTACCAGTCAACAGGAACTGAGAGAATTTCTCCCCATCACCACTTTCCAAAGGAACACTCTTAAGTATGCCCTGA
CAGGGGAGAAATGAAGGATCTGCGTGCAGCAGTTTATTAAGATTATGGCAAGTTATGAACTGACATAACCTACCCTACTG
ATTTTATGGAGGTCATCAGTATTGGCAAGACCAGAGAGAATTTTCATCCAAGCTATGACAGTGAAGATTACCTGGCTGTT
CATTGTATTATATGTGAAGAGGCCAAATACAAATTGTGCACAGTGAAAAAGATCTTCATGGGTACTAGGGAATCCCTAAT
CTAGTGACTCATGGTATTCACACCATCTTCTACCTTGATCCCCTCATCAAGGTGAATGATATCATTCAGAATGATTTGGA
GACTGACTAGATTACTGAATTCATCAAGTTTACTACTGGTAACCTATGTATGGTGATTGGAGGTGCTAAGCTAAAAGAAT
TGGTGTGATCACCAACACAGAG

Alignment

ORF - retro_pvam_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.32 %
• Parental protein coverage: 74.52 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIKID
          GPK.H.K...APKH.ML.KLT.V..P.PST....LRE.LP...F.RN.LKYALTG.....IC.Q.FIKI.
Retrocopy GPKMHRKCGVAPKH*MLSKLTSVSVPHPSTSQQELREFLPITTFQRNTLKYALTGEK*R-ICVQQFIKIM

Parental  -GKVRTDVTYPAGFMDVISIDKTGENFRLVYDTKGRFAVHRITTEEAKYKLCKVRKIFVGTK-GIPHLVT
          .GK..TD.TYP..FM.VISI.KT.ENF...YD.....AVH.I..EEAKYKLC.V.KIF.GT..GIP.LVT
Retrocopy <GKL*TDITYPTDFMEVISIGKTRENFHPSYDSEDYLAVHCIICEEAKYKLCTVKKIFMGTR<GIPNLVT

Parental  HDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANL-GRIGVITNRE
          H...TI.Y.DPLIKVND.IQ.DLET..IT.FIKF.TGNLCMV.GGA.L..RIGVITN.E
Retrocopy HGIHTIFYLDPLIKVNDIIQNDLETD*ITEFIKFTTGNLCMVIGGAKL<KRIGVITNTE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1158 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 159 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Ailuropoda melanoleuca	ENSAMEG00000005805	14 retrocopies	retro_amel_1003, retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Callithrix jacchus	ENSCJAG00000004192	2 retrocopies	retro_cjac_19, retro_cjac_361,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus	ENSFCAG00000012041	11 retrocopies	retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Gorilla gorilla	ENSGGOG00000023079	18 retrocopies	retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Myotis lucifugus	ENSMLUG00000011685	5 retrocopies	retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Macaca mulatta	ENSMMUG00000003295	7 retrocopies	retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338, retro_mmul_43, retro_mmul_97,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus	ENSMUSG00000031320	13 retrocopies	retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Pongo abelii	ENSPPYG00000020462	24 retrocopies	retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes	ENSPTRG00000022025	9 retrocopies	retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Pteropus vampyrus	ENSPVAG00000012882	21 retrocopies	retro_pvam_1021, retro_pvam_1082, retro_pvam_1158 , retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,