RetrogeneDB ID: retro_tbel_2986

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_125804:6911..7372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSTBEG00000002543
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_tbel_2986
TTACTGGCTGAAGAAAATTTTGTTATGGTGATGATTTTTACTCTAGTGACAGCTGTGCAAGAAAAATTAAATGAAATAGT
AGATCAGATAGAAGCTAGAGGAGAGGAAGAAAAGAAACAGAAAAGGAAGCAGAATAAGCCGAAGAGCAATTATTCCATGG
CACTCCTGTTACGATTGAAAATTTCTTGAGCTGAAAGGCCAAGTGTGATGCAGAACTCTTGGAAGTGAAAAAGAAAAGGA
TGGAAGAAGAAGAGCAAGCAGGAAAAGGCAAATTAAATGGGAAGCAGCTGTTTGAAACAGATCATAGTCTTGATACTTGT
GATATCCAATTGTTGGAGGCTGCTGGAAACAATGTGGAGGTAGATGAGTCTTAGTTCCAGGAAATGGATGACTTGGAGCT
AGAGGATGATGAAGATGATCCAGACTATAATCCTGCTGACCCAGAGAGTGACTCAGCTGAC

Alignment

ORF - retro_tbel_2986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.97 %
• Parental protein coverage: 71.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQAEENLGMVMIFTLVTAVQEKLNEIVDQIKTRREEEKKQK-EKEAEEAEKQLFHGTPVTIENFLSWKAK
          L.AEEN..MVMIFTLVTAVQEKLNEIVDQI..R..EE.K...EKEAE.AE.QLFHGTPVTIENFLS.KAK
Retrocopy LLAEENFVMVMIFTLVTAVQEKLNEIVDQIEARG-EEEKKQ<EKEAE*AEEQLFHGTPVTIENFLS*KAK

Parental  FDAELLEIKKKRMKEEEQAGKSKLSGKQLFETDHNLDTSDIQFLEDAGNNVEVDESLFQEMDDLELEDDE
          .DAELLE.KKKRM.EEEQAGK.KL.GKQLFETDH.LDT.DIQ.LE.AGNNVEVDES.FQEMDDLELEDDE
Retrocopy CDAELLEVKKKRMEEEEQAGKGKLNGKQLFETDHSLDTCDIQLLEAAGNNVEVDES*FQEMDDLELEDDE

Parental  DDPDYNPADPESDSTD
          DDPDYNPADPESDS.D
Retrocopy DDPDYNPADPESDSAD

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_2986 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2986 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986 , retro_tbel_4366,