RetrogeneDB ID: retro_tbel_3438

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_140437:1370..1844(+)
• 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_3438
AAGAAGCACGCTCAGTGTGCAATATCCAATGTGTTCACCATGTTTGACCAGTCACAGATTCAGGAGTTCAAAGAGGCCTT
CAACATGACTGATCAAAACAGCAATGGTTTCATCAACAAGGATTTGCATGATATGTTTGCATTGCTAGGGATGAGGCCCA
CTGATGCATACCTCAATAAATGATGCCATGATAAATGAGGCTCCAGGTCCCATCAATTTACTATGTTCCTCACCACATTT
GGGGAGAAGCTAAATGGCATAGATTCCGAAGATGTCAGAAATGCTTTTGCCTATTTTGATGAAAAAACAACAGGAATCAT
TCAGGAGGATTACCTGAGAGAGCTGCTGACAACAATGGAAAGATAGTTTCACAGATGTGGTGGGGGACAGAGAAGCACCT
ATTGACAAAAAAGGAATTTCAATTACATTCAGTTCACACGCATCCTTAAACATGGAGCAAAAGATCACAATGAC

Alignment

ORF - retro_tbel_3438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKRPQRATSKVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDAYLDAMMNEAPGPI
          .K..Q.A.S.VF.MFDQSQIQEFKEAFNM.DQN..GFI.K.DLHDM.A.LG..PTDAYL........G..
Retrocopy KKHAQCAISNVFTMFDQSQIQEFKEAFNMTDQNSNGFINK-DLHDMFALLGMRPTDAYLNK*CHDK*GSR

Parental  N--FTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTM-GDRFTDEEVDELYREAPI
          ...FTMFLT.FGEKLNG.D.EDV.RNAFA.FDE..TG.IQEDYLRELLTTM..D.FTD...D...REAPI
Retrocopy SHQFTMFLTTFGEKLNGIDSEDV-RNAFAYFDEKTTGIIQEDYLRELLTTM>KDSFTDVVGD---REAPI

Parental  DKKG-NFNYIEFTRILKHGAKDKDD
          DKKG.NFNYI.FTRILKHGAKD..D
Retrocopy DKKG<NFNYIQFTRILKHGAKDHND

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_3438 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3438 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,