RetrogeneDB ID: retro_tbel_1027

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3612:629731..630297(-)
• Located in intron of: ENSTBEG00000000377

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000013600
• Aliases: None
• Description: None

Sequence

>retro_tbel_1027
GAACAGCTCTCTCCAGTTACAGCAAACTCACATGTTTATTACAGAAGGGGACTGGCTCTGAAAAAAATGATTTCACATTG
CATCTTGAGCAATTTCACAGATCTGATCGTGATTAATGAAGACCATAAAACACCAAATGGACTTATTTTGAGTCCCTTGC
CAAATGGCCCAACTGCTCATTTTAAAATGAGCAGGGTTCGTCTTTGTAACAAAATGAAGAGAAGAGGCAAGGACTCCACA
GAGCATACAGCCTAAATACTACTGAGTAATTTTACAGCGTGGCTAGGTCCTTTAGTTGGATGTATGTTTGCATCTCTCTT
CCCCTGGGGTCCTCAATTTATCGGCTGGCAGGCGGTCAGAGTCCACAGTCAGCCGGATTATATTTTCTTCATATTTCACA
GATACATATTTAAGAGTGAAAAGAAAGTGGGAATTCTGGAACTTGGATCACAGTTTACCTTAAAATTAAGATCGCTTCAA
AAAGGAACTTTTGATTCTAAAAATGGAGAGTATGAATGTGTCCCTAATCCCAGGAAATGGATACTAGTGGAAGAAAATTC
CATTTA

Alignment

ORF - retro_tbel_1027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.26 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQLSTVIPNSHVYYRRGLALKKIIPQCISRDFTDLIVINEDRKTPNGLILSHLPNGPTAHFKMSSVRLRK
          EQLS.V..NSHVYYRRGLALKK.I..CI...FTDLIVINED.KTPNGLILS.LPNGPTAHFKMS.VRL..
Retrocopy EQLSPVTANSHVYYRRGLALKKMISHCILSNFTDLIVINEDHKTPNGLILSPLPNGPTAHFKMSRVRLCN

Parental  EIKRRGKDPTEHKPEIILNNFTTRLGHSIGRMFASLFPHDPQFIGRQVATFHNQRDYIFFRFHRYIFKSE
          ..KRRGKD.TEH...I.L.NFT..LG...G.MFASLFP..PQFIG.Q....H.Q.DYIFF.FHRYIFKSE
Retrocopy KMKRRGKDSTEHTA*ILLSNFTAWLGPLVGCMFASLFPWGPQFIGWQAVRVHSQPDYIFFIFHRYIFKSE

Parental  KKVGIQELGPRFTLKLRSLQKGTFDSKYGEYEWVHKPR-EMDTSRRKFHL
          KKVGI.ELG..FTLKLRSLQKGTFDSK.GEYE.V..PR.EMDTS.RKFHL
Retrocopy KKVGILELGSQFTLKLRSLQKGTFDSKNGEYECVPNPR<EMDTSGRKFHL

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_1027 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1027 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027 , retro_tbel_2204, retro_tbel_2279, retro_tbel_63,