RetrogeneDB ID: retro_tbel_2437

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110633:29246..29509(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R1A
• Ensembl ID: ENSTBEG00000001193
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286]

Sequence

>retro_tbel_2437
AGTGACCAGTCATTCCCAGAGATAGATGAAGATCTGATTCCCAGACCCCTTCTCAAGTCTATTTGTCAGTGTTTCCAGGG
CAACAGAAGATGACAAGGACCACAACCAGAATGAAATAGCTCCACATGATAGTTGAACATCACCTGGAGAAATGGTAGCA
AGGGGAGAAGCCTAAGGGAGCTGCCAGGAGCTCAGGGAACCACCCACGTGGGCTCACAGGCACAGCAGTGGAGTCAAGGC
TGTGCATCTCTGGGGCAGCTCAG

Alignment

ORF - retro_tbel_2437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.22 %
• Parental protein coverage: 68.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDQSSPEIDEDRIPNPLLKST-LSMSPRQRKKMTRTTPTMKELQMMVEHHLGQQ-QQEEPEGAAKSTGTQ
          SDQS.PEIDED.IP.PLLKS..LS..P.Q..KMTRTT..MK.L.M.VEHHL....Q.E.P.GAA.S.G..
Retrocopy SDQSFPEIDEDLIPRPLLKSI<LSVFPGQ-QKMTRTTTRMK*LHMIVEHHLEKW*QGEKPKGAARSSGNH

Parental  ESCPPGITDTEAESRLGTSGTAQ
          ...P.G.T.T..ESRL..SG.AQ
Retrocopy ---PRGLTGTAVESRLCISGAAQ

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_2437 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2437 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 6 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000010159	1 retrocopy	retro_fcat_1131,
Homo sapiens	ENSG00000135447	2 retrocopies	retro_hsap_1633, retro_hsap_896,
Gorilla gorilla	ENSGGOG00000008380	1 retrocopy	retro_ggor_1231,
Pongo abelii	ENSPPYG00000004608	1 retrocopy	retro_pabe_774,
Pan troglodytes	ENSPTRG00000005044	2 retrocopies	retro_ptro_1138, retro_ptro_619,
Tupaia belangeri	ENSTBEG00000001193	20 retrocopies	retro_tbel_1191, retro_tbel_1233, retro_tbel_1251, retro_tbel_1264, retro_tbel_138, retro_tbel_1881, retro_tbel_2036, retro_tbel_2437 , retro_tbel_2574, retro_tbel_2720, retro_tbel_3243, retro_tbel_3316, retro_tbel_3377, retro_tbel_3380, retro_tbel_3414, retro_tbel_3426, retro_tbel_4551, retro_tbel_537, retro_tbel_669, retro_tbel_899,