RetrogeneDB ID: retro_mluc_2253

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL430149:418409..418933(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMLUG00000028735
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSMLUG00000011685
• Aliases: None
• Description: None

Sequence

>retro_mluc_2253
CTGGCTCATGGTCCCAAGAAGCATCTGAGGTGTGTAGTGGCTCCAGAGCGTTGGGTGCTGGATACACTGACGGTGTGTTT
GCTTCTCGGCCATCTACCGGTCCCCACAAGCTGAGAGAATGTCTCCCTCTCATCATTTTCTATGGAACAGACTTAATTAT
GCCCTAACAGGAGATGAAGGAAAGATCAGCACGCAGCGGTTTATTAAGATTGATGACAAGGTTCAAACCGAGGTAACCCA
CCCCGCTGGCTTTATGGATGTAATCAGCATTGACAAGACCAGCGAGAATTTCCGTCTGATCTGTGACACCAAGGGCCGCT
TTGCTGTTCATCGGATCGTGCCTGAGGAGGCCAAGTACAGGTTGTGCAAAGTGAGGAGGGTCTTTGTGGGCACAAGAGGA
ATCCTTGATCGGGTGGCCTATGATGTTCACACCATCAGCTTACCTGGATCCCCTCAAGGTAAATGACACCATTCAGGTTG
ACTTGGAGACTGGCAAAATGACTGATGTTATCAAGTGTGGCACC

Alignment

ORF - retro_mluc_2253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 67.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARGPKKHLKRVAAPKHWMLDKLT-GVFAPRPSTGPHKLRECLPLIIF-LRNRLKYALTGDEVKKICMQR
          .A.GPKKHL..V.AP..W.LD.LT.GVFA.RPSTGPHKLRECLPLIIF.L.NRL.YALTGDE..KI..QR
Retrocopy LAHGPKKHLRCVVAPERWVLDTLT<GVFASRPSTGPHKLRECLPLIIF<LWNRLNYALTGDE-GKISTQR

Parental  FIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPH
          FIKID.KV.T..T.PAGFMDVISIDKT.ENFRLI.DTKGRFAVHRI.PEEAKY.LCKVR..FVGT.GI..
Retrocopy FIKIDDKVQTEVTHPAGFMDVISIDKTSENFRLICDTKGRFAVHRIVPEEAKYRLCKVRRVFVGTRGILD

Parental  LVTHDARTIRYP-DPLIKVNDTIQIDLETGKITDFIKFDT
          .V..D..TI..P.DPL.KVNDTIQ.DLETGK.TD.IK..T
Retrocopy RVAYDVHTISLP>DPL-KVNDTIQVDLETGKMTDVIKCGT

Legend:

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

Expression

RNA-Seq

Myotis lucifugus was not studied using RNA-Seq expression data.

ChIP-Seq

Myotis lucifugus was not studied using ChIP-Seq data.

EST

Myotis lucifugus was not studied using EST data.

TSS

Myotis lucifugus was not studied using FANTOM5 data.

Lab

retro_mluc_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Myotis lucifugus 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 21 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
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,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Dipodomys ordii	ENSDORG00000008571	4 retrocopies	retro_dord_289, retro_dord_650, retro_dord_68, retro_dord_745,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Loxodonta africana	ENSLAFG00000002654	4 retrocopies	retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii	ENSMEUG00000007969	16 retrocopies	retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
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,
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,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Procavia capensis	ENSPCAG00000000761	3 retrocopies	retro_pcap_334, retro_pcap_35, retro_pcap_360,
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,
Ictidomys tridecemlineatus	ENSSTOG00000028692	8 retrocopies	retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,
Tarsius syrichta	ENSTSYG00000003137	16 retrocopies	retro_tsyr_1159, retro_tsyr_1167, retro_tsyr_118, retro_tsyr_1302, retro_tsyr_1333, retro_tsyr_1774, retro_tsyr_1792, retro_tsyr_1931, retro_tsyr_1936, retro_tsyr_2116, retro_tsyr_409, retro_tsyr_440, retro_tsyr_522, retro_tsyr_529, retro_tsyr_750, retro_tsyr_917,
Vicugna pacos	ENSVPAG00000010952	4 retrocopies	retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,