RetrogeneDB ID: retro_tbel_3001

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_126109:51779..52782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFAP1
• Ensembl ID: ENSTBEG00000005050
• Aliases: None
• Description: microfibrillar-associated protein 1 [Source:HGNC Symbol;Acc:7032]

Sequence

>retro_tbel_3001
AAGAAAGTAGTGGAGCCTGCGGTGGTAGGAGAAAGTGGCTCCGAGGTAGAAGGAGACGCTTGGTGCATGGAACGAGAAAA
TGGCAGTGAAGAAGAGGAGGAGGAAATTGGAGATGATGAGCAAAGAAAGGGGTGCCATGGCATGATGCGTCCAGCACAGG
AGAGGAAAAATGAAGAGATGGAAGTCATGGAGGTCGAAGATGAGGGACGTTCAGGAGAAGAGTCAGAATTAGAATTGGAA
CATGAAGAGTACACGGACAGCGAAGATGAGATGGAGCCTCGCCTTACTCCAGTCTTCATTCAAAAGAAGGACTGAGTAAC
AGTTCAAGAACGTGAGGCTGAAGCCTTGAAACAGGAGCTGGAGCAGGAAGCAAAACACATGGCTGGGGAGAGTTGCAAGT
ACACTCTCGAGATTGTAGAAGAGGAGACCAAGGAAGAACTGGAGGAGAATAAGTGGTCCTTGGCTGCACTGGAAGCACTC
AATACTGATGATGAAAATGATGAGGAGGAGTATGAGGCATGGAAAGTCTGGGAACTAAAACAAATCAAGAGGGACAGAGA
AGAACGAGAAGCACTTCAGAAAGAGAAAGCAGAAACTGAATACATGCGAAACCTGAGTGAGGAAGAGGAGAGAGCTGAGC
TTCGGGCAAATTGCAAAGCCCATCACCCACAAAGCTGTGAAGGGCAAATACAAGTGCTTACAGAAGTATTATCACCAGAG
TGGCCTCCTTTCATGGATGGAGATGAAGTATACAAGACAGATTTCAGTGCGCCCTATTCTGGAGGATCATTTCACCAAAA
CAATTCTTTCTAAAATCATGCAGGTCAAGAACTTCGGCCGTTCTGGCAGTACTAAATATGTTCATCTTGTTGATCAAGAC
ACCACATCCCTCGACTCAGCTTGGGGCCAAGAGAGTGCCCAAAACACAAAGTTCTGTAAACAAAAGGCAGCAGGAGCACA
AGATGTATTTGAACCACCCTCTTCCAAGAAGCAGAAAACCACC

Alignment

ORF - retro_tbel_3001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKIVEPEVVGESDSEVEGDAWRMEREDSSEEEEEEI-DDEEIERRRGMMRQRAQERKNEEMEVMEVEDEG
          .K.VEP.VVGES.SEVEGDAW.MERE..SEEEEEEI.DDE......GMMR..AQERKNEEMEVMEVEDEG
Retrocopy KKVVEPAVVGESGSEVEGDAWCMERENGSEEEEEEIGDDEQRKGCHGMMRP-AQERKNEEMEVMEVEDEG

Parental  RSGEESESESEYEEYTDSEDEMEPRLKPVFIRKKDRVTVQEREAEALKQKELEQEAKRMAEERRKYTLKI
          RSGEESE.E.E.EEYTDSEDEMEPRL.PVFI.KKD.VTVQEREAEALKQ.ELEQEAK.MA.E..KYTL.I
Retrocopy RSGEESELELEHEEYTDSEDEMEPRLTPVFIQKKD*VTVQEREAEALKQ-ELEQEAKHMAGESCKYTLEI

Parental  VEEETKKELEENKRSLAALDALNTDDENDEEEYEAWKVRELKRIKRDREDREALEKEKAEIERMRNLTEE
          VEEETK.ELEENK.SLAAL.ALNTDDENDEEEYEAWKV.ELK.IKRDRE.REAL.KEKAE.E.MRNL.EE
Retrocopy VEEETKEELEENKWSLAALEALNTDDENDEEEYEAWKVWELKQIKRDREEREALQKEKAETEYMRNLSEE

Parental  ERRAELRAN-GKVITNKAVKGKYKFLQKYYHRGAFF-MDEDEEVYKRDFSA-PTLEDHFNKTILPKVMQV
          E.RAELRAN..K.IT.KAVKGKYK.LQKYYH...........EVYK.DFSA.P.LEDHF.KTIL.K.MQV
Retrocopy EERAELRAN>AKPITHKAVKGKYKCLQKYYHQSGLL<FMDGDEVYKTDFSA>PILEDHFTKTILSKIMQV

Parental  KNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTKFFKQKAAGVRDVFERPSAKKRKTT
          KNFGRSG.TKY.HLVDQDTTS.DSAWGQESAQNTKF.KQKAAG..DVFE.PS.KK.KTT
Retrocopy KNFGRSGSTKYVHLVDQDTTSLDSAWGQESAQNTKFCKQKAAGAQDVFEPPSSKKQKTT

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_3001 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3001 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013870	1 retrocopy	retro_dord_22,
Myotis lucifugus	ENSMLUG00000013000	2 retrocopies	retro_mluc_1384, retro_mluc_2298,
Mus musculus	ENSMUSG00000048222	2 retrocopies	retro_mmus_1147, retro_mmus_2346,
Mus musculus	ENSMUSG00000068479	2 retrocopies	retro_mmus_2386, retro_mmus_2638,
Otolemur garnettii	ENSOGAG00000010206	1 retrocopy	retro_ogar_1784,
Rattus norvegicus	ENSRNOG00000015984	1 retrocopy	retro_rnor_83,
Sarcophilus harrisii	ENSSHAG00000014628	1 retrocopy	retro_shar_107,
Ictidomys tridecemlineatus	ENSSTOG00000006967	2 retrocopies	retro_itri_1105, retro_itri_1494,
Tupaia belangeri	ENSTBEG00000005050	2 retrocopies	retro_tbel_3001 , retro_tbel_3246,