RetrogeneDB ID: retro_mmur_564

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_3873:51501..52013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB3
• Ensembl ID: ENSMICG00000015668
• Aliases: None
• Description: high mobility group box 3 [Source:HGNC Symbol;Acc:5004]

Sequence

>retro_mmur_564
GGTGACCCCAAGAAACCAAAGGGCAAGATGTCTGCTTATGCCTTCTTTGTGCAGACGTGCAGAGAAGAACATAAGAAGAA
AAACCCAGAGTCCCTGTCAATTTGGCAGAATTTTCCAAGAAGTGCTCTGAGAGGTGGAAGACAATGTCTGGGAAAGAGAA
GTCTAAATTTGATGAAATGGCAAAGGCGGATAAAGCCCGCTATGATCGGGAAATGAAGGATTATGGACCAGCTAAGGGAG
GAAAGAAGAAGAAGGACCCTAATGCCCCCAAAAGGCCACCGTCTGGATTCTTCCTGTTCTGTTCAGAATTCCGCCCCAAG
ATCAAATCTGCAAACCCTGGCATCTCTATTGGAGATGTGGCAAAAAAGCCGGGTGAGATGTGGCATAACTTAAGTGACAG
TGAAAAGCAGCCTTACATCACTAAGGCTGCAAAGCTGAAGAAGTATGAGAAGGATGTTGCTGACTATAAGTCTAAAGGAA
AGTTTGATGGCGCAAGGGTCCCGCTAAAGTTG

Alignment

ORF - retro_mmur_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 88.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDPKKPKGKMSAYAFFVQTCREEHKKKNPE-VPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD
          GDPKKPKGKMSAYAFFVQTCREEHKKKNPE.VPVN.AEFSKKCSERWKTMSGKEKSKFDEMAKADK.RYD
Retrocopy GDPKKPKGKMSAYAFFVQTCREEHKKKNPE<VPVNLAEFSKKCSERWKTMSGKEKSKFDEMAKADKARYD

Parental  REMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLSDSEKQPY
          REMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKS.NPGISIGDVAKK.GEMW.NLSDSEKQPY
Retrocopy REMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSANPGISIGDVAKKPGEMWHNLSDSEKQPY

Parental  ITKAAKLKEKYEKXXXXYKSKGKFDGAKGPNKI
          ITKAAKLK.KYEK....YKSKGKFDGA..P.K.
Retrocopy ITKAAKLK-KYEKDVADYKSKGKFDGARVPLKL

Legend:

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

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_564 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_564 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005150	2 retrocopies	retro_btau_190, retro_btau_38,
Canis familiaris	ENSCAFG00000028715	1 retrocopy	retro_cfam_1537,
Choloepus hoffmanni	ENSCHOG00000005005	2 retrocopies	retro_chof_1891, retro_chof_2010,
Cavia porcellus	ENSCPOG00000000601	2 retrocopies	retro_cpor_1432, retro_cpor_384,
Equus caballus	ENSECAG00000020596	1 retrocopy	retro_ecab_890,
Echinops telfairi	ENSETEG00000015689	4 retrocopies	retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
Felis catus	ENSFCAG00000024624	4 retrocopies	retro_fcat_1480, retro_fcat_1504, retro_fcat_265, retro_fcat_865,
Loxodonta africana	ENSLAFG00000025877	1 retrocopy	retro_lafr_893,
Microcebus murinus	ENSMICG00000000573	1 retrocopy	retro_mmur_1529,
Microcebus murinus	ENSMICG00000007144	7 retrocopies	retro_mmur_11, retro_mmur_1452, retro_mmur_154, retro_mmur_182, retro_mmur_40, retro_mmur_428, retro_mmur_664,
Microcebus murinus	ENSMICG00000015668	4 retrocopies	retro_mmur_564 , retro_mmur_60, retro_mmur_853, retro_mmur_994,
Myotis lucifugus	ENSMLUG00000010926	4 retrocopies	retro_mluc_1055, retro_mluc_1989, retro_mluc_215, retro_mluc_529,
Monodelphis domestica	ENSMODG00000005735	7 retrocopies	retro_mdom_1257, retro_mdom_1508, retro_mdom_1883, retro_mdom_1952, retro_mdom_587, retro_mdom_698, retro_mdom_831,
Mustela putorius furo	ENSMPUG00000011606	2 retrocopies	retro_mputfur_138, retro_mputfur_26,
Oryctolagus cuniculus	ENSOCUG00000005986	7 retrocopies	retro_ocun_1033, retro_ocun_1913, retro_ocun_1914, retro_ocun_534, retro_ocun_568, retro_ocun_891, retro_ocun_931,
Procavia capensis	ENSPCAG00000001945	1 retrocopy	retro_pcap_328,
Pteropus vampyrus	ENSPVAG00000000219	1 retrocopy	retro_pvam_356,
Sarcophilus harrisii	ENSSHAG00000002916	2 retrocopies	retro_shar_139, retro_shar_316,
Sus scrofa	ENSSSCG00000012745	3 retrocopies	retro_sscr_1094, retro_sscr_466, retro_sscr_467,
Tupaia belangeri	ENSTBEG00000003068	18 retrocopies	retro_tbel_1002, retro_tbel_1230, retro_tbel_1579, retro_tbel_1700, retro_tbel_1819, retro_tbel_2543, retro_tbel_2730, retro_tbel_3261, retro_tbel_3476, retro_tbel_3623, retro_tbel_3781, retro_tbel_408, retro_tbel_410, retro_tbel_4203, retro_tbel_4209, retro_tbel_4299, retro_tbel_605, retro_tbel_698,
Tursiops truncatus	ENSTTRG00000000205	2 retrocopies	retro_ttru_1187, retro_ttru_372,
Vicugna pacos	ENSVPAG00000000096	2 retrocopies	retro_vpac_245, retro_vpac_434,