RetrogeneDB ID: retro_meug_558

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold136587:3389..4091(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H3
• Ensembl ID: ENSMEUG00000013734
• Aliases: None
• Description: general transcription factor IIH, polypeptide 3, 34kDa [Source:HGNC Symbol;Acc:4657]

Sequence

>retro_meug_558
TTCTTGTATTCTGGAAAGAACTGAAGATTTGGAGACTTATTTGGTGATCCTGGCAACAACTTTGGTGAGTATAATTCTTC
AGGTAATAAGGATGGAAAATATGAGTTATTAAACTGCAGAAATGAAGAAATTGCTGAAGAGATTAGAGATCTCATGATCA
AAATGACATTGGAGGGGCAGTGTACAGAAACGCTGCTGGCAGGATCTCTCGCAAAAGCATTCTGTTATATTCAAAGAATG
GGCAAGGAAGTAAAAGATAACCAAGAAATGAAGTTGAGAACATTGGTCGTTAAGGTTGCAGGAGACAATGCGGTGCAATA
TGTTAATCTCGTGAATGTCCCCTTTGCATCACAGAAACAGAATATTGTGATTGACTCTTGTGTCTTAGATACTGATTCAG
GGCTTCTCTGCCAGGTTTGTATTACAGGGGGCATATACATGAAGGTGCCCCAGATGCCATTTCTTCTTTAGCATTTATTA
TGGGTATTTCTTCCTGATCAAGACCAATAGTCTCAGTTAAATCTCTCCCTTCCTATTCACAGTGACTACAAAGCTGCTTG
CTTCTAACAAAGAAATCTCATTGAAATTGGTTATGTCTGTTCTGTATGTTTGTCAATATTCTACAATTTCAGCTCTATTT
GCATCACATGGGAGACAGCTTTTAAGATTTCACTGCCTCCTGTTCTGAAAATCAAGAAGAAA

Alignment

ORF - retro_meug_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.74 %
• Parental protein coverage: 77.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLYPGKNWKFGDLFGDPGNSSAEYNPFRSKDGKYELLTAANEAITEEIKDLMTKSDMEGQRTETLLAGSL
          FLY.GKN..FGDLFGDPGN...EYN....KDGKYELL...NE.I.EEI.DLM.K...EGQ.TETLLAGSL
Retrocopy FLYSGKN*RFGDLFGDPGNNFGEYNSSGNKDGKYELLNCRNEEIAEEIRDLMIKMTLEGQCTETLLAGSL

Parental  AKALCYIHRMGKEVKDNKEMKSRILVIKAAEDSALQYMNFMNVIFAAQKQNIVIDACVLDTDSGLLQQAC
          AKA.CYI.RMGKEVKDN.EMK.R.LV.K.A.D.A.QY.N..NV.FA.QKQNIVID.CVLDTDSGLL.Q.C
Retrocopy AKAFCYIQRMGKEVKDNQEMKLRTLVVKVAGDNAVQYVNLVNVPFASQKQNIVIDSCVLDTDSGLLCQVC

Parental  DITGGIYLKVPQMPSLLQYLLWVFLPDQDQRSQLNLPPPIHVDYRAACFCHRNLIEIGYVCSVCLSIFCS
          .ITGGIY.KVPQMP.LL..LLWVFLPDQDQ.SQLNL..PIH.DY.AACF..RNLIEIGYVCSVCLSIF..
Retrocopy -ITGGIYMKVPQMPFLL*HLLWVFLPDQDQ*SQLNLSLPIHSDYKAACF*QRNLIEIGYVCSVCLSIFYN

Parental  FSPICTTCETAFKISLPPVLKAKKK
          FS.IC.T.ETAFKISLPPVLK.KKK
Retrocopy FSSICITWETAFKISLPPVLKIKKK

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_558 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_558 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006219	2 retrocopies	retro_chof_1726, retro_chof_2064,
Loxodonta africana	ENSLAFG00000007300	1 retrocopy	retro_lafr_292,
Macropus eugenii	ENSMEUG00000013734	1 retrocopy	retro_meug_558 ,
Myotis lucifugus	ENSMLUG00000004319	1 retrocopy	retro_mluc_183,
Monodelphis domestica	ENSMODG00000023728	1 retrocopy	retro_mdom_1915,
Tupaia belangeri	ENSTBEG00000011048	8 retrocopies	retro_tbel_1645, retro_tbel_1820, retro_tbel_2555, retro_tbel_3550, retro_tbel_3894, retro_tbel_3931, retro_tbel_4065, retro_tbel_4293,
Tarsius syrichta	ENSTSYG00000007444	1 retrocopy	retro_tsyr_1126,
Tursiops truncatus	ENSTTRG00000007259	1 retrocopy	retro_ttru_1357,