RetrogeneDB ID: retro_dord_661

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_4955:7311..8289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pias3
• Ensembl ID: ENSDORG00000013427
• Aliases: None
• Description: protein inhibitor of activated STAT 3 [Source:MGI Symbol;Acc:MGI:1913126]

Sequence

>retro_dord_661
GTTACCCCTCACTCACCACCATCTCCTGTTGGTTCTGTGCTGCAGCAACCATCTCTTCCACTTCCTCCTGACCATCCTGA
GGTGCAGCTCACAAACTTGCCCTTTTATGATATCCTTAAGGTTCTCATCAAACCCACCAGTTTAGTTAAAAGCAGCATTC
CGCCATTTCAAGAGAACTTCTTTAGTTTTGCTCTGACACCTCAAGAAGTTAGAAAGATCCGCATATCAAAACACTCTTTG
CCAGGTGGCAGAATAAATTATGGAGTCCAAGTGCAGCTGAGACTTTGCCTGGTAGAGACAAGTTGCCCTCAAGAAGATAA
CTACCCCAACAGACTATGTATAAAAGTAAACGGATGGCTGTTTCCTTTGCCTGGCTCTGCATCCTCACCTAAAAGTGGGA
TTGAACAGAAGTGCCCTGGGCGCCCGTTGAATATTACATCTTTAGTTAGATTGTCTTCGGCTGTGCCCAATCGGATTTCT
ATTTCTTGGGCATCTGAAATTGGGAAGAATCACTCCATGTCTGTATATCTTGTAGAAAAGCTCACCTCAGCCACGTTACT
ACAGAGATTAAACTGTACTGTTAGTAATCCAGACCAATCCAGAGCACTAATTAAAGAAAAACTTACTGCGGATCCTGATA
GTGAAGTTGCTGTGACTAGTCTTCAGGTATCGCTGGTGTGCCCTTTAGGAAAAATGAGGCTGACAGCCCCATGCCGTGCA
GTGACATGTACACACCTGCAGTGTTTTGATGCTGCCGTCTACCTACAAATGAATGAGAAGAAACTCACCTGGATTTGTCC
TGTGTGTGACCAAAAAGCTGCCTACGAAAATCTGATATTAGATGGGCTTTTTATGGAAATTCTCAGTGCCTGTTCAGAGG
TGGATGAGATTGAATTCCAAAAAGATGGCGTTTGGTGTCCAGTGAGGCTGAAGAAAGAAGCTATGCAGGTTCCCAGTCCA
CCACATGCAAACTTAGAA

Alignment

ORF - retro_dord_661 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.33 %
• Parental protein coverage: 52.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTPGTLLGPKREVDLHPPLPQPV-HPDVTMKPLPFYEVYGELIRPTTLASTSSQRFEEAHFTFALTPQQV
          .TP.....P...V...P.LP.P..HP.V....LPFY.....LI.PT.L...S...F.E..F.FALTPQ.V
Retrocopy VTPHSPPSPVGSVLQQPSLPLPPDHPEVQLTNLPFYDILKVLIKPTSLVKSSIPPFQENFFSFALTPQEV

Parental  QQILTSREVLPGAKCDYTIQVQLRFCLCETSCPQEDYFPPNLFVKVNGKLCPLPGYLPPTKNGAEPKRPS
          ..I..S...LPG....Y..QVQLR.CL.ETSCPQED..P..L..KVNG.L.PLPG.....K.G.E.K.P.
Retrocopy RKIRISKHSLPGGRINYGVQVQLRLCLVETSCPQEDNYPNRLCIKVNGWLFPLPGSASSPKSGIEQKCPG

Parental  RPINITALARLSATVPNTIVVNWSSEFGRNYSLSVYLVRQLTAGTLLQKLRAKGIRNPDHSRALIKEKLT
          RP.NIT.L.RLS..VPN.I...W.SE.G.N.S.SVYLV..LT..TLLQ.L......NPD.SRALIKEKLT
Retrocopy RPLNITSLVRLSSAVPNRISISWASEIGKNHSMSVYLVEKLTSATLLQRLNCT-VSNPDQSRALIKEKLT

Parental  ADPDSEVATTSLRVSLMCPLG-MRLTVPCRALTCAHLQSFDAALYLQMNEKKPTWTCPVCDKKAPYESLI
          ADPDSEVA.TSL.VSL.CPLG.MRLT.PCRA.TC.HLQ.FDAA.YLQMNEKK.TW.CPVCD.KA.YE.LI
Retrocopy ADPDSEVAVTSLQVSLVCPLGKMRLTAPCRAVTCTHLQCFDAAVYLQMNEKKLTWICPVCDQKAAYENLI

Parental  IDGLFMEILNSCSDCEEIQFMEDGSWCPMKPKKEASEVCPPPGYGLD
          .DGLFMEIL..CS...EI.F..DG.WCP...KKEA..V..PP...L.
Retrocopy LDGLFMEILSACSEVDEIEFQKDGVWCPVRLKKEAMQVPSPPHANLE

Legend:

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

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_661 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013427	1 retrocopy	retro_dord_661 ,