RetrogeneDB ID: retro_meug_1372

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold383893:694..1349(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSMEUG00000009291
• Aliases: None
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_meug_1372
ATGTTCGCCAAAGGCAAAGTCTCAGCAGTCCCCTAGAACAAGCAGGATGTGTAAAAGTTGGCTTTGTACATCGATGTATA
CTTGCTACAAGTGGGAGCCCAGAAGTCAGGCCAGACTTTTTTGTCCAAGATCTGATGGGAAAAAAAAAAAATCAAGTTAG
GAGAATCTTCTGGATTCTTACATTTGTGGTGGTGTGTTTTCTGAGACCTTTACTGTGCCACTCCTGAAGAGACGAAGCAC
TTGTGACCATTTGAGTGAAGGCAAGGCCTTTTATTATTACAGTGCACCTGCAGCCTCAAGTCCTATACTGGGCAATATTT
CACCAAATGATGTCAAGCCTGGAGGCCCCATCCCTTGTAGCTTCTTTCAGGGTCCTTAAGGTTCCCAGCCCTTGCCCTAC
GCACACCCTGCACTCCACAATTCTAACAGTATGATGAGGCCCCACAGTCAGCCCTTTATGTCACCTCCATATGCAGGTGG
CCCCAGGTCCCCCATCAGAATGGGAAACAAGCCCCTTGGAGGAATTCCCAGCACACAACCATTACAGCCCTACTCAATGG
ACCAGATGAGACAAGAAGGACACCCCAACATGGGAGGCTCAATGAAAAGAATGAACACCCAACAAGGAATAGGACCACTG
GGTACTGGTCCACAG

Alignment

ORF - retro_meug_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.32 %
• Parental protein coverage: 55.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFAKGKGSAVPSDGQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNIT-LGEPPGFLHSWWCVFWDL
          MFAKGK.SAVP...Q...KLALY...YLL.VGAQKS.QTFLS.I.W......LGE..GFLH.WWCVF.DL
Retrocopy MFAKGKVSAVP*NKQDV*KLALYIDVYLLQVGAQKSGQTFLSKI*WXXXXXKLGESSGFLHLWWCVF*DL

Parental  YCAAPE-RRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPAPH
          YCA.PE.RR.TC.H.SE.KAF..YSA.AA.SP.LGNI.PND..PGGPIP..FFQGP.GSQP.P.A.PA.H
Retrocopy YCATPE>RRSTCDHLSEGKAFYYYSAPAASSPILGNISPNDVKPGGPIPCSFFQGP*GSQPLPYAHPALH

Parental  NANSMMGPHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRG
          N.NSMM.PHSQPFMSP.YAGGPR.PIRMGN.P.GG.P.TQPL.P.SMD..RQ.GHPNMGGSM.RMN...G
Retrocopy NSNSMMRPHSQPFMSPPYAGGPRSPIRMGNKPLGGIPSTQPLQPYSMDQMRQEGHPNMGGSMKRMNTQQG

Parental  MGPMGPGPQ
          .GP.G.GPQ
Retrocopy IGPLGTGPQ

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_1372 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1372 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005029	1 retrocopy	retro_cjac_3827,
Homo sapiens	ENSG00000157216	6 retrocopies	retro_hsap_1302, retro_hsap_1384, retro_hsap_2155, retro_hsap_2319, retro_hsap_2539, retro_hsap_3721,
Macropus eugenii	ENSMEUG00000009291	1 retrocopy	retro_meug_1372 ,
Oryctolagus cuniculus	ENSOCUG00000005903	1 retrocopy	retro_ocun_252,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,