RetrogeneDB ID: retro_mluc_642

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429769:20770344..20771030(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC3
• Ensembl ID: ENSMLUG00000008662
• Aliases: None
• Description: Histone deacetylase [Source:UniProtKB/TrEMBL;Acc:G1PBZ1]

Sequence

>retro_mluc_642
TATGCAAAGAGCCTTAATGCCTTCAATGTGGGCGATGACTGCCCAGTGTTTCCCGGGCTTTTTGAGTTTTGTTCCCATTA
CACATGCCCATCTCTGCAAAGAGCAACCCAGCTGAACAACAAGATCTGTGATATTGCCATTAACTGGGCTGGAGGTCTGC
ACCATGCCAAGAAGTTTGAGGCCTCTGGCTTCTGCTATGTCAATGACATTGTGATTGGCATCCTGCAGCTGCTCAAGTAT
CACCCTCAGGTGCTCTACATTGATATTGACATCCACCATGGTGACGGGGTTCTTGAAGCCTTCTACGTCACTGCCCGGGT
CATGACAGTATCCTTCCACAAGTATGGAAATTACTTCTTTCCTAGCACAGGTGACATGTATGAAGTTGGAGCATAGGGAG
GCCGCTACTACGGTCTCAATGTGCCCCTGTGGGATGGCATTGATGACCAGAGTTACAAGCACCTTTTCCAGCTGATTATC
AACCAGGTGGTAGACTTCTACCAACCCACGTGCATTGTTCTTCAGTGTGGAGCTGACTCTCTGGGCTGTGATGGATTGGG
CTGCTTCAACCTCAGCATTCGAGGACATGGGGATTACGTCAAATATGTCAAGAGCATCAATATTCCTCTACTGGTGCTAG
TGGTGGTGGTTTTACTCTCCGAAATGTTGCCCAGTGCTGGAGACAT

Alignment

ORF - retro_mluc_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDI
          ..KSLNAFNVGDDCPVFPGLFEFCS.YT..SLQ.ATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDI
Retrocopy YAKSLNAFNVGDDCPVFPGLFEFCSHYTCPSLQRATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDI

Parental  VIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLN
          VIGIL.LLKYHP.VLYIDIDIHHGDGV.EAFY.T.RVMTVSFHKYGNYFFP.TGDMYEVGA..GRYY.LN
Retrocopy VIGILQLLKYHPQVLYIDIDIHHGDGVLEAFYVTARVMTVSFHKYGNYFFPSTGDMYEVGA*GGRYYGLN

Parental  VPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPL
          VPL.DGIDDQSYKHLFQ..INQVVDFYQPTCIVLQCGADSLGCD.LGCFNLSIRGHG..V.YVKS.NIPL
Retrocopy VPLWDGIDDQSYKHLFQLIINQVVDFYQPTCIVLQCGADSLGCDGLGCFNLSIRGHGDYVKYVKSINIPL

Parental  LVL-GGGGYTVRNVARCWTY
          LVL..GGG.T.RNVA.CW..
Retrocopy LVL<SGGGFTLRNVAQCWRH

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_642 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Myotis lucifugus	ENSMLUG00000008662	1 retrocopy	retro_mluc_642 ,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000012588	1 retrocopy	retro_mmul_49,
Procavia capensis	ENSPCAG00000010817	1 retrocopy	retro_pcap_298,
Ictidomys tridecemlineatus	ENSSTOG00000016240	1 retrocopy	retro_itri_1661,
Tupaia belangeri	ENSTBEG00000007520	1 retrocopy	retro_tbel_1811,