RetrogeneDB ID: retro_tbel_3088

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_129653:86267..86678(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL12B
• Ensembl ID: ENSTBEG00000009299
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827]

Sequence

>retro_tbel_3088
AGAAAGTGTCCTTAGTGTGCAGCATCCAACATGTTTGCCAGGTTTGACCAGGCACAGATTTAGGAGTTTAAAGAGGCCTT
CAACATGATTGATCAAAACAGAAATGGTTTTACCAACAAGGAAGATTTGCATGATATGCTTGCCTCACTGGGGAAGAATC
CAACTTATGAGTATCTGGATGCCGTGATGAAAGAGGATCCTGGTCCCATCAATTTCGTCATGTTTCTCACAATGTCTGGT
GAAAGGTTAAATGGCACAGATCCAGAAGATGTCATCAGAAACACTTTTGCTTCCTTTGGTGAAGACGCAACTGGCACCAT
TCAGGAGGATTACCTGAAAGAGCTGCTGAAAACAGTGGGAGATCATTCTCCAGATGAGGAAGTGAACGAACTGTACTGAG
AAGCACCTATA

Alignment

ORF - retro_tbel_3088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.64 %
• Parental protein coverage: 85.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKRPQRATSKVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDAYLDAMMNEAPGPI
          RK.P..A.S..FA.FDQ.QI.EFKEAFNMIDQNR.GF..KEDLHDMLASLGKNPT..YLDA.M.E.PGPI
Retrocopy RKCP*CAASNMFARFDQAQI*EFKEAFNMIDQNRNGFTNKEDLHDMLASLGKNPTYEYLDAVMKEDPGPI

Parental  NFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEVDELYREAPI
          NF.MFLTM.GE.LNGTDPEDVIRN.FA.F.E.ATGTIQEDYL.ELL.T.GD...DEEV.ELY.EAPI
Retrocopy NFVMFLTMSGERLNGTDPEDVIRNTFASFGEDATGTIQEDYLKELLKTVGDHSPDEEVNELY*EAPI

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_3088 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3088 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 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Oryctolagus cuniculus	ENSOCUG00000021304	1 retrocopy	retro_ocun_900,
Rattus norvegicus	ENSRNOG00000015733	2 retrocopies	retro_rnor_1614, retro_rnor_2718,
Tupaia belangeri	ENSTBEG00000009299	4 retrocopies	retro_tbel_1294, retro_tbel_1629, retro_tbel_3088 , retro_tbel_3438,
Tarsius syrichta	ENSTSYG00000010418	9 retrocopies	retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,