RetrogeneDB ID: retro_tbel_4535

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_88922:8722..9065(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPH
• Ensembl ID: ENSTBEG00000011867
• Aliases: None
• Description: centromere protein H [Source:HGNC Symbol;Acc:17268]

Sequence

>retro_tbel_4535
CTTGCATTAGACAGGATGCAACTTTCAAGTACACCTACAAAAAGCCTAGAGAAAACTGACATAAAAAATAGTGTGCTCAT
GGATAGCACGAAATATGTGTTAAAGCTAAATAAATTAATAATGAAATCATAGCAAGAATCTTGGGATATAGAGGAAAAAC
TGCTTGCTGTTAAAAAGAAGAAATTGCAGTGAAAACAAACTTCAGAAAGTAAGCTTTAAGAAATACATATTGAAAAGAAC
AAATAGAAATATGATTTGGAAAATTCAGACAAGATAAAAGACCACACAACTAAACTGACAGATGGAGATACAGATTACTA
AAGTTATTCAACATGTGTTCCAG

Alignment

ORF - retro_tbel_4535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 57.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LALDRVRLSNALQKNLEKIDVKNSVLIDNMNQVLKLSKLIMKAQQESWDLEEKLLAVRKKRLQLKQASES
          LALDR..LS....K.LEK.D.KNSVL.D....VLKL.KLIMK..QESWD.EEKLLAV.KK.LQ.KQ.SES
Retrocopy LALDRMQLSSTPTKSLEKTDIKNSVLMDSTKYVLKLNKLIMKS*QESWDIEEKLLAVKKKKLQ*KQTSES

Parental  KLLEIQTEKNKQKDDLDSMENSDKI-KSIQQNLQMEIQIATVIQHVFQ
          KL.EI..EKNK.K.DL...ENSDKI.K..Q.N.QMEIQI..VIQHVFQ
Retrocopy KL*EIHIEKNK*KYDL---ENSDKI>KTTQLN*QMEIQITKVIQHVFQ

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_4535 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4535 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007717	1 retrocopy	retro_cfam_961,
Choloepus hoffmanni	ENSCHOG00000011338	2 retrocopies	retro_chof_1939, retro_chof_982,
Monodelphis domestica	ENSMODG00000025601	1 retrocopy	retro_mdom_1859,
Mustela putorius furo	ENSMPUG00000014646	1 retrocopy	retro_mputfur_240,
Sarcophilus harrisii	ENSSHAG00000007822	4 retrocopies	retro_shar_805, retro_shar_806, retro_shar_807, retro_shar_809,
Tupaia belangeri	ENSTBEG00000011867	2 retrocopies	retro_tbel_4318, retro_tbel_4535 ,
Tarsius syrichta	ENSTSYG00000002098	1 retrocopy	retro_tsyr_199,