RetrogeneDB ID: retro_tbel_4520

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_87785:1003..1294(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL3
• Ensembl ID: ENSTBEG00000000664
• Aliases: None
• Description: peptidylprolyl isomerase (cyclophilin)-like 3 [Source:HGNC Symbol;Acc:9262]

Sequence

>retro_tbel_4520
ACTGAAAGAGGAGGTAACAGTATCTGGGGGTAAAAAGTTTGAAGGTGATACATATAGTGAATATCTTAAGCATAATGTTA
GAGCCATTGTATCTATGGCTAATCGTGGTCCAAACACCAATTGTCTCAGTTCTTCATCACCTATTGGAAACAACCACATT
TGGACATAAAATACACTGTATTTGGAAAGGTAATAGATGATCTGAAGACTCTAGATGAATTGGAGAAGTTACAGTAAGTG
AGAAGACATTATCGACCTCTTAATGATGTACACATTAAGGATATAACTATG

Alignment

ORF - retro_tbel_4520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.8 %
• Parental protein coverage: 93.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGRGGNSIWG-KKFE-DEYSEYLKHNVRGVVSMANNGPNTNG-SQFFITYGKQPHLDMKYTVFGKVIDGL
          T.RGGNSIWG.KKFE.D.YSEYLKHNVR..VSMAN.GPNTN..SQFFITY.KQPHLD.KYTVFGKVID.L
Retrocopy TERGGNSIWG>KKFEGDTYSEYLKHNVRAIVSMANRGPNTNC<SQFFITYWKQPHLDIKYTVFGKVIDDL

Parental  ETLDELEKLPVNEKTYRPLNDVHIKDITI
          .TLDELEKL......YRPLNDVHIKDIT.
Retrocopy KTLDELEKLQ*VRRHYRPLNDVHIKDITM

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4520 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4520 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005917	1 retrocopy	retro_amel_1458,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180,
Dasypus novemcinctus	ENSDNOG00000002364	1 retrocopy	retro_dnov_2477,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575,
Monodelphis domestica	ENSMODG00000015037	1 retrocopy	retro_mdom_1025,
Tupaia belangeri	ENSTBEG00000000664	1 retrocopy	retro_tbel_4520 ,