RetrogeneDB ID: retro_tbel_4616

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_93220:9882..10750(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSTBEG00000017616
• Aliases: None
• Description: actin, alpha 2, smooth muscle, aorta [Source:HGNC Symbol;Acc:130]

Sequence

>retro_tbel_4616
CATGTGGGCGATGAGGCCCAGAGCAAGAGAGGCATGCCGACCTTAAAGTACCCTATTGAGCACGGCGTTGTCACCACCTG
GGACGACATGGAGAAGACCTGGCACCACACTGTCCCATGAGTGGCATGGAGCCCCGAGGAGCATCCTGTGCTGCTGACTG
AGGCTCCTCTGAATCCCAAGGCCGACCGGGAAAAGATGACCCAGATCACATTTGAGACCAACACCCCAGCCATGTACGTG
GCCCTCCAGGTGGTGCTGTCCCTGTGTGCCTCTGGCCGTACCACTGGCGTCGTGACGGACTCCGGTGATGGGGTCACCCA
CACTGTGCCCATCTATGAGGGTATCCTTCCCCATGCCATCCTGCGTCTGGACCTGGCTGGCCGGGACCTGACGGACGACC
TCATGAAGATCCTCGCGGAGCGTGACTACAGCTTCACCACCACAGCCAAGCGGGACACTGTGCGTGACATCAAGGACGAG
CTGTGCTATGTCGCCCTGGACTTCGAGCAGGAGACGGCCACCACAGCCCCCGGCTCCTCCCTGGAAAAGAGCCACGGTCA
GGCGATCACCATCGGCCATGAGGCTTCCGCTGTCCTGAGGCGCCCTGCCAGCCATCTTTCCTGGGCATGGAATCTCGTGG
CGTCCACGAAACCACCTTCGACTCCAGCACGAAGTGCGAAGTGGACATCGGCAAGGACCTGAGTGCCAACACGCCCTGTC
TGGGGCACCACCATGGCTCCAGGCCTTGCCGACAGAATGCAGAGGGAGATAACCTCCCGGCACCGAGCACCACGACGGTG
GAGGTCGTCGCTCCCCCGAGCGCAAGTACTGTGTGACTGGTGGCTCCACCCTGGCCTCGCTGTCCACC

Alignment

ORF - retro_tbel_4616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 79.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREKMTQI
          .VGDEAQSKRG..TLKYPIEHG..T.WDDMEK.W.H.........PEEHP.LLTEAPLNPKA.REKMTQI
Retrocopy HVGDEAQSKRGMPTLKYPIEHGVVTTWDDMEKTW-HHTVP*VAWSPEEHPVLLTEAPLNPKADREKMTQI

Parental  MFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKI
          .FET.N.PAMYVA.Q.VLSL.ASGRTTG.V.DSGDGVTH.VPIYEG..LPHAI.RLDLAGRDLTD.LMKI
Retrocopy TFET-NTPAMYVALQVVLSLCASGRTTGVVTDSGDGVTHTVPIYEGI-LPHAILRLDLAGRDLTDDLMKI

Parental  LTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNER-FRCPETL
          L.ER.YSF.TTA.R..VRDIK..LCYVALDFE.E.AT.A..SSLEKS.....GQ.ITIG.E..FRCPE..
Retrocopy LAERDYSFTTTAKRDTVRDIKDELCYVALDFEQETATTAPGSSLEKSH----GQAITIGHEA<FRCPEAP

Parental  FQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYAN-NVLSG-GTTMYPGIADRMQKEITAL-APSTMKIK
          .QPSF.GMES.G.HETT..S..KC..DI.KDL.AN...LSG.GTTM.PG.ADRMQ.EIT...APST....
Retrocopy CQPSFLGMESRGVHETTFDSSTKCEVDIGKDLSAN<HALSG<GTTMAPGLADRMQREITSR<APSTTTVE

Parental  IIAP-PERKYSVWIGGSILASLST
          ..AP.PERKY.V..GGS.LASLST
Retrocopy VVAP<PERKYCV-TGGSTLASLST

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_4616 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4616 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 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000010781	1 retrocopy	retro_tbel_422,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616 ,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,