RetrogeneDB ID: retro_meug_1748

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold56415:5149..5757(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CA
• Ensembl ID: ENSMEUG00000005323
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9281]

Sequence

>retro_meug_1748
CTGCAGGGTTCCCAGCTTGGCAAGAACATGAAGCTGATTGAGAATAAGACCTGTGGCCTGTATCTTAAATCATAGGAGAT
CTTCCTGGGCCAGACCATCCTCCTACAGCTTGAGTTGCTGCTCAAGAACTGCAGTGACATCCATGGTCAGTACTATGACC
TGCTCAGATTGCTTGAGTAGGAGGTTTTCCCCCTGAAAGCAACTACATCTTCCCAGGGGACCATGTGGACTAGATCAAAT
AGTCCCTGGGAACGATCTGCTACTGGCCTACAAGGTCAAATATCCACAGAACTCCCTACTTGTCCATGGTACTCATGAGT
GTGTCAGCATCAACTGCTTCTATAATAAATACAGGAGACACCACAACATAAAGATATGGAAAACTTTCATAGACTGCTTC
AACTACCTGGCCAGTACCATCATCATGCAGAAAATTTTCTGGTGTCATGGAGGACTGTCTCCACACCTGGAGCTCATGGA
GCAGATGTGGTATATCATGAGACCCACAGATATGTCAGACAAGAGCTGTTCCATGTCCTGCTGTGCTCAAATCCTGACAA
AGATGTACAAGGCCACAAGGAAATGACCTTGATGTCTCCTTTACTTAC

Alignment

ORF - retro_meug_1748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.44 %
• Parental protein coverage: 63.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFE-YGGFPPESNY
          .QGS..GKN..L.EN...GL.LKS.EIFL.Q.ILL.LE..LK.C.DIHGQYYDLLRL.E..GGFPPESNY
Retrocopy LQGSQLGKNMKLIENKTCGLYLKS*EIFLGQTILLQLELLLKNCSDIHGQYYDLLRLLE<VGGFPPESNY

Parental  LFLGDYVDRGKQSLETIC-LLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCF
          .F.GD.VD..K.SL.TIC.LL.AYK.KYP.N..L..G.HEC.SIN....FY....R..NIK.WKTF.DCF
Retrocopy IFPGDHVD*IK*SLGTIC<LL-AYKVKYPQNSLLVHGTHECVSIN---CFYNKYRRHHNIKIWKTFIDCF

Parental  NCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPD-QGLLCDLLWSDPDKDVQGWGE-NDRGVS
          N.L....I...KIF.CHGGLSP.L..MEQ...IMRPTD..D.Q.L...LL.S.PDKDVQG..E.ND..VS
Retrocopy NYL-ASTIIMQKIFWCHGGLSPHLELMEQMWYIMRPTDMSD<QELFHVLLCSNPDKDVQGHKE<NDLDVS

Parental  FTF
          FT.
Retrocopy FTY

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_1748 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1748 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Dasypus novemcinctus	ENSDNOG00000007986	3 retrocopies	retro_dnov_2565, retro_dnov_525, retro_dnov_872,
Macropus eugenii	ENSMEUG00000005323	1 retrocopy	retro_meug_1748 ,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,