RetrogeneDB ID: retro_meug_1250

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold34066:6913..7654(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLDND1
• Ensembl ID: ENSMEUG00000001155
• Aliases: None
• Description: claudin domain containing 1 [Source:HGNC Symbol;Acc:1322]

Sequence

>retro_meug_1250
GCCACAGCATTGATAATTGTTTGTGTGTTCAACCTCTTTCTACCATCTATATGCCAGCACCAATTGGCACAGATTTCTGA
TATGAATATCGAAGTCCAGCACCAGAAAATTTCAGTGATTTAAACAAAATCAGGGAAGAACTTGTTGACAATAATCCAGA
TGAAAAGACTTATAATGACTTATTTTTCTGGTATAATGGCAGATTGGAATTGTGGAGAAGGTGTATCACCTTGCCCAACA
AAAGCACACTTTGATATGGTTCTCCAGAAAAGAAAGAGTCATCTGACTTGATCATAGAATGTTCCAGTTTTACACTGTCA
GAGCAATTCACGGAGAAGTATCTAGAGCCTGGAAACCACAACACTGAGACTGATCTACTTCGGACCTATCTTTGGCTCTG
CCAGTTCCTTTTTCCTTTTGTTAGACTAGGTTTGATGTACTTTGGGGCTTTGATTGGACTTTGTGCCTGTGCCTGCTGGA
GTCTGTGTCCAGCTATTGCCACAGAAGTCCTTCATTTCCTTGCAGGTTTGTGTATACTGAGCTCAGTAAGTTGCTATGTT
GCTAGTATGGAACTATTTCAGCAGAAGCTGCAGCTGCCTGAGAATGTAAAGGGTGAATTTGGTTGGTTCTTCTGCCCGGC
CTGTGTCTCAGTCCTCTTGTAGTTCATAGCTGCTATACTCTTCATCTGGGCACCATACTAATCGAAAAGAGCACACACTA
ATGATGGCCTATCAGGTGGCA

Alignment

ORF - retro_meug_1250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.6 %
• Parental protein coverage: 98.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATALVIACVLSL-ISTIYMAASIGTDFWYEYRSPAPENFSDLNKIREEFFDSESDEKTYNDLLFRYNGTV
          ATAL.I.CV..L..STIYM.A.IGTDF.YEYRSPAPENFSDLNKIREE..D...DEKTYNDL.F.YNG..
Retrocopy ATALIIVCVFNL<LSTIYMPAPIGTDF*YEYRSPAPENFSDLNKIREELVDNNPDEKTYNDLFFWYNGRL

Parental  GLWRRCITVPNKSTPGYSSPEKTESSDFVTECSSFTLSEQFMEKYLEPGNHNTGIDLLRTYLWRCQFLLP
          .LWRRCIT.PNKST..Y.SPEK.ESSD...ECSSFTLSEQF.EKYLEPGNHNT..DLLRTYLW.CQFL.P
Retrocopy ELWRRCITLPNKSTL*YGSPEKKESSDLIIECSSFTLSEQFTEKYLEPGNHNTETDLLRTYLWLCQFLFP

Parental  FVSLGLMCFGALIGLCACACRSLYPTIATGVLHFLAGLCTLGSVSCYVAGIELLHQKLQLPENVKGEFGW
          FV.LGLM.FGALIGLCACAC.SL.P.IAT.VLHFLAGLC.L.SVSCYVA..EL..QKLQLPENVKGEFGW
Retrocopy FVRLGLMYFGALIGLCACACWSLCPAIATEVLHFLAGLCILSSVSCYVASMELFQQKLQLPENVKGEFGW

Parental  SFCLACVSAPLQFMAAALFIWAA-RTNRKEYTLMKAYRVA
          .FC.ACVS..L.F..AA.....A..TNRKE.TLM.AY.VA
Retrocopy FFCPACVSVLL*FI-AAILFIWA>HTNRKEHTLMMAYQVA

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1250 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1250 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001155	1 retrocopy	retro_meug_1250 ,
Myotis lucifugus	ENSMLUG00000013947	1 retrocopy	retro_mluc_1099,
Oryctolagus cuniculus	ENSOCUG00000017858	1 retrocopy	retro_ocun_1085,