RetrogeneDB ID: retro_mluc_2011

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429987:1826852..1827362(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSMLUG00000026303
• Aliases: None
• Description: None

Sequence

>retro_mluc_2011
GGGATGTTCCTTAGTCATGCAAACCTGGCAGGAAGAGCACAAGAAGAAACAACACCCAATCAGAGTCTTTCCCTCAATTT
CGCCAAATTCTCCAAGAATTGTTCAAAGAGATGGATGACCATATCTGCAAAAGAAAAGTCAAAGTTTGAAGATATGTCAA
AGAGTAACAAAGCTCTCTATGTTAAGGAAATAAAAAATTATATTTCTCCCAAAGTGATAAGGACAGAAAAAAAGATCCCA
AAGCTCCTCAAAGGCCTCCATCTGCCTTCTTCTTGTTTTTCTCTGAATATTGCCCAAAGATCAAAAGTGAACACCCTCAT
TTATCCAATGGGGATACTGCAAAAAGAGTTGGGGGAAATGGGTCTGAACAGTCAGCCAAAGATAAGCAACCATTTGAACA
AAAAGGAGCTACACTAAAGGAGAAATATGGAAAAAATATTCCTGCATCCTGGGCCCAGTGCAAAAGTGAAGTGGAAAGAA
GGGCCCTGCAGGCCAACATGCTCAAGGAAG

Alignment

ORF - retro_mluc_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.71 %
• Parental protein coverage: 83.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKMSSYAFFVQCREEHKKKHPDSSVNFSEFSKKCSEKWKTMSAKEKSKFEDMAKSDKARYDREMKNYVPP
          G...S.A.......E........S.NF..FSK.CS..W.T.SAKEKSKFEDM.KS.KA.Y..E.KNY..P
Retrocopy GMFLSHANLAGRAQEETTPNQSLSLNFAKFSKNCSKRWMTISAKEKSKFEDMSKSNKALYVKEIKNYISP

Parental  K-GDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAK
          K..DK...KKDP.AP.RPPSAFFLF.SE..PKIKSEHP.LS.GDTAK..G...SEQSAKDKQP.EQK.A.
Retrocopy K<SDK-DRKKDPKAPQRPPSAFFLFFSEYCPKIKSEHPHLSNGDTAKRVGGNGSEQSAKDKQPFEQKGAT

Parental  LKEKYEKDIAAYRAKGKSEV-GKKGPG-RPTGSKK
          LKEKY.K.I.A..A..KSEV.GKKGP..RPT.S.K
Retrocopy LKEKYGKNIPASWAQCKSEV<GKKGPA<RPTCSRK

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_2011 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 23 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Callithrix jacchus	ENSCJAG00000005112	2 retrocopies	retro_cjac_2555, retro_cjac_832,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Loxodonta africana	ENSLAFG00000010417	3 retrocopies	retro_lafr_1096, retro_lafr_1142, retro_lafr_595,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Myotis lucifugus	ENSMLUG00000010926	4 retrocopies	retro_mluc_1055, retro_mluc_1989, retro_mluc_215, retro_mluc_529,
Myotis lucifugus	ENSMLUG00000025979	17 retrocopies	retro_mluc_1062, retro_mluc_1103, retro_mluc_1446, retro_mluc_1584, retro_mluc_1591, retro_mluc_1608, retro_mluc_1615, retro_mluc_1773, retro_mluc_1798, retro_mluc_2013, retro_mluc_2201, retro_mluc_2460, retro_mluc_506, retro_mluc_551, retro_mluc_800, retro_mluc_809, retro_mluc_953,
Myotis lucifugus	ENSMLUG00000026303	4 retrocopies	retro_mluc_1113, retro_mluc_1381, retro_mluc_1726, retro_mluc_2011 ,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Mustela putorius furo	ENSMPUG00000001919	9 retrocopies	retro_mputfur_1134, retro_mputfur_1167, retro_mputfur_1379, retro_mputfur_1475, retro_mputfur_1631, retro_mputfur_1633, retro_mputfur_1644, retro_mputfur_940, retro_mputfur_989,
Mus musculus	ENSMUSG00000054717	23 retrocopies	retro_mmus_1477, retro_mmus_1745, retro_mmus_1974, retro_mmus_1975, retro_mmus_2269, retro_mmus_2527, retro_mmus_2528, retro_mmus_2529, retro_mmus_2530, retro_mmus_2531, retro_mmus_2843, retro_mmus_2884, retro_mmus_3248, retro_mmus_3426, retro_mmus_461, retro_mmus_626, retro_mmus_642, retro_mmus_796, retro_mmus_861, retro_mmus_901, retro_mmus_902, retro_mmus_904, retro_mmus_905,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Oryctolagus cuniculus	ENSOCUG00000000074	1 retrocopy	retro_ocun_1829,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Ictidomys tridecemlineatus	ENSSTOG00000023980	2 retrocopies	retro_itri_1720, retro_itri_880,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,