RetrogeneDB ID: retro_tbel_2841

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_120899:41273..41814(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTSV
• Ensembl ID: ENSTBEG00000016406
• Aliases: None
• Description: cathepsin V [Source:HGNC Symbol;Acc:2538]

Sequence

>retro_tbel_2841
TACAAGTCAAGCCTTATTCAGAAATTACCTGAGTCTCTGGACTGGAGAGAGAAGGGATGTGTTACTGAAGTGAAATATCA
GGAGGCATGTATTACTTGCTGGGCTTTCAGTGCTGTAGGGGCCCTGGAAGCACAGCTGAAGCTGAAAACAGGAAAGCTGG
TGTCTCTCAGTGCACAGAAACTGGTAGACTGCTCCACTTCAATATATGAATAAAGGCTGCAATGGAGGCTTCATGACAGG
CTTTTCAATACTTCATTGATAACAATGGCATTGATTCAGAAGCTTCCTACCCCTACCCCTTTCCATCCGTGGATGGAAAG
TGTCATATGACTCGAAAAATCGTGCTGCCGCATGTTCCGAGTACATGGAACTTCCTTCTGGCAGTGAAGAGACCCTGAAA
GAAGCCGTGGCCAATAAAGGGCCTGTGTCTATTGCTATAGATGCGAGTCATTCTTCTTTCTTCTTCTACAGAAGTGGCAT
CTACTATGAACCATCTTGTACTCAGACTATGAATCATGGTGTACTAACAGTTGGCTATGGT

Alignment

ORF - retro_tbel_2841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.69 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FHAPLLLQAPKSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGKLISLSEQNLVDCSR-RQG
          ....L....P.S.DWREKG.VT.VK.Q..C..CWAFSA.GALE.Q...KTGKL.SLS.Q.LVDCS.....
Retrocopy YKSSLIQKLPESLDWREKGCVTEVKYQEACITCWAFSAVGALEAQLKLKTGKLVSLSAQKLVDCST>QYM

Parental  NLGCQGGLM-DNAF-QYIKDNGGLDSEESYPY--KGMDGTC-QYKAEWAVANDTGFVDIPASQEKALMKA
          N.GC.GG.M.D..F.QY..DN.G.DSE.SYPY.....DG.C..Y......A........P...E..L..A
Retrocopy NKGCNGGFM<DRLF<QYFIDNNGIDSEASYPYPFPSVDGKC<SYDSKNRAAACSEYMELPSGSEETLKEA

Parental  VASVGPISVAIDAGHASFQFYKDGIYYEPDCSSENLDHGVLVVGYG
          VA..GP.S.AIDA.H.SF.FY..GIYYEP.C......HGVL.VGYG
Retrocopy VANKGPVSIAIDASHSSFFFYRSGIYYEPSC-TQTMNHGVLTVGYG

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_2841 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2841 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345, retro_chof_141, retro_chof_1464, retro_chof_2392, retro_chof_383, retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186, retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841 ,