RetrogeneDB ID: retro_tbel_1879

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5922:186265..187553(-)
• Located in intron of: ENSTBEG00000009820

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSTBEG00000007876
• Aliases: None
• Description: mitogen-activated protein kinase 6 [Source:HGNC Symbol;Acc:6879]

Sequence

>retro_tbel_1879
GCACATGAACTTGAACAGAGGCAGCTGATTTTAGAATCTGTTCCTGTTGTACACAAGAAAGATCATCAAGAACTTCTCAG
CATAATTCCAGTTTACATTAGAAATTTCATGACTGAGCCACACAAACCTTTAACTCAGATGCTTCCAGAAATTAGTCAAA
AAGCATGAGGTTTCCTGGAACAAATATTGACATTTAGCCCCATGGATTGGTTAACAGCAGAGGAAGTGCTCTCCCACACT
CACATGAGCAAATATTCTTTTCCAATGGAAGAGTCAATTTCAAGTCTTTTTTTTCATATTGAAGATGTAGTTGATAATAT
TTTGCTTATGGATGAAACTCACAGTCACATTTATAACTGGGAAAGGTACCATGACTGTCAGTTTTCAAAACATGACTGGC
CTATACATAACAACTTTGATATTGATGAAGTTCAGCTTGCCCCAAGAGCTCTGTCTGGTGTTACTTATAAAGGATAAGTA
CAAGTTTATCCTCAAAAATATTTATATGGAGATCAGGAAAAGTATCTGGAGGATCCTATTTTTGATACTAATTATTCTAC
TGAACCTTGATGGCAGTACCCAGATCACCATGAAAACAAATAATGTGATCTGGAGTGTAGCCAGATTGACAAAATGAGGT
CATCATCATATTTAGATAACTTACTTTGGAAAGAGAGTGAAGTTAATCATTGCTATGAACCCAAGCTTATTGTAGATCTT
TCCAATTGGAAAGAACAAAGCAAAGAAAAATCTGATAAGAAAGGCAAGTCAAAATGTGAAAGGAATGGATTAGAAAGGCC
CAGCTAGCACCTAAGGAAGCATCAAGACTGGTTGAAAAGGAAAGGAAAAAGAATCCCGGATTTGATTTTGATTCTTTTAT
CACAGGAACTATTCAGCTTAGTTCACAACACAAGCCTACTGACATTGTTGATAAATTAAACGACTTGAATAGCTCAGTGT
CCCAACTATATTTGAAAAGTTTGATATCAAAGTTAGTAAACCCAGAGAAGCAGGAAAAAGGAATGGCAAACTTGGCTCAG
TTAGAAGCCGTATATGAGTCTCCCTGCGACAGCAGTTTGTGAGTTGGGGGAAGGACAGTTTTCTCATCAATCAGTTTTGT
TACCAGGTGAGGAAAGATGAGCAGGCTCAGAAGGAAAACACTTATGCTAGTTACTTGAACAAGTTCTTCAGCAAGAAAGG
AGATTCTGAAATACTAGAAACTGAACCAGTAGAAGATGGGAAGCATGGGGAGAGAGGAAATGAGGAAGCCTTCCTGAACA
ACAGTGGG

Alignment

ORF - retro_tbel_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 60.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDR
          AHELEQ.QLILES.PVVH..D.QELLS.IPVYIRN.MTEPHKPLTQ.LP.IS..A..FLEQILTFSPMD.
Retrocopy AHELEQRQLILESVPVVHKKDHQELLSIIPVYIRNFMTEPHKPLTQMLPEISQKA*GFLEQILTFSPMDW

Parental  LTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWER-HDCQFSEHDWPIHNNFD
          LTAEE.LSH..MS.YSFPM.E.ISS...HIED.VD.ILLMDETHSHIYNWER.HDCQFS.HDWPIHNNFD
Retrocopy LTAEEVLSHTHMSKYSFPMEESISSXXXHIEDVVDNILLMDETHSHIYNWERYHDCQFSKHDWPIHNNFD

Parental  IDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDTNYSTEPCWQYPDHHENKYCDLECGHTC
          IDEVQL.PRALS.VT....VQV.P.KYL.GD.EKYLEDP.FDTNYSTEP.WQYPDHHENK.CDLEC....
Retrocopy IDEVQLAPRALSGVTYKG*VQVYPQKYLYGDQEKYLEDPIFDTNYSTEP*WQYPDHHENK*CDLECSQI-

Parental  NYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCERNGLV-KAQIALEEASQL
          ..KMRSSSYLDNL.W.ESEVNH.YEPKLI.DLSNWKEQSKEKSDKKGKSKCERNGL..KAQ.A..EAS.L
Retrocopy -DKMRSSSYLDNLLWKESEVNHCYEPKLIVDLSNWKEQSKEKSDKKGKSKCERNGLE<KAQLAPKEASRL

Parental  AEKEREKNQGFDFDSFIAGTIQLSSQREPADVVDKLNDLNSSVSQLELKSLISKSVSREKQEKGMANLAQ
          .EKER.KN.GFDFDSFI.GTIQLSSQ..P.D.VDKLNDLNSSVSQL.LKSLISK.V..EKQEKGMANLAQ
Retrocopy VEKERKKNPGFDFDSFITGTIQLSSQHKPTDIVDKLNDLNSSVSQLYLKSLISKLVNPEKQEKGMANLAQ

Parental  LEALYQSSWES-QFVSGAEDCFLISQFCCEVRKDEHAEKENTYTSYLDKFFSRKEDSEMLETEPVEDGKL
          LEA.Y.S...S.QFVS...D.FLI.QFC..VRKDE.A.KENTY.SYL.KFFS.K.DSE.LETEPVEDGK.
Retrocopy LEAVYESPCDS<QFVSWGKDSFLINQFCYQVRKDEQAQKENTYASYLNKFFSKKGDSEILETEPVEDGKH

Parental  GERGNEEAFLNNSG
          GERGNEEAFLNNSG
Retrocopy GERGNEEAFLNNSG

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_1879 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1879 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879 , retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,