RetrogeneDB ID: retro_itri_1105

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393376.1:3585579..3586514(-)
• Located in intron of: ENSSTOG00000010540

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFAP1
• Ensembl ID: ENSSTOG00000006967
• Aliases: None
• Description: microfibrillar-associated protein 1 [Source:HGNC Symbol;Acc:7032]

Sequence

>retro_itri_1105
GCACTCATGAAGCAATTGCCCATTCAGTCTAAGGCTGGGGCCATACTGGTTCGAAGTGAGAATGGTGAGATTTCAATGGA
AAAGATAAAGGTAAAACGTTATGTATCTGGAAAGAAGCCAGACTATGCCCCATGGAGTCTTCAGATGAGAAGGATAAAGA
ATTTCAGTTCATTAAGAAAACCCAAGAACTAGAAGCACAACTGGAGGAACAGGAGGAGGATTCATCTAGTGACCCCTGGC
TGCGGCATTTATAGAATCGTGAAGATGTGGAAGAGAGATTGGCCCAAAATCCCAAAATAGTATACCTAAAGTAGTAGGAG
AAAGTGACTCAGAAGTAGGAGATGCTTGGTGCATGGAACAAGAAGTAGCAGTGAAGAAAAAGAGGAAAATATTGATGAGG
ATGTAGAGCTGCACCATGGCATGATGTGTCAATGAGGGCAGGAGAGAAAAAATTGAAGAGATGGAAGTCATGGAGGTGTA
AGATGAAGAACATTCTGGGGAGGAGTCAGAATCAGAGTCTGAATATGAAGATTATACATACAATGAAGATGAGATGGAGC
CTTGCTTTACGCCATTCTTATTTGAAAGAAGGACCAAATGACAGTTCAAAAATGTGAGGCTGAAGCATTGAAACAGAAAG
AGATGGAGCAAGGAGCAAAGCCCATGGCTGAAGGGAGGCGAAATTACACACTCAAGATTGTAGAAGAGGAGACCAAGAAA
GAGCTGGAGGAAAACAAGTGTTCCTGGCTGCACTGGATGTACTCAGTACTGACAGTGAAAATGATGAGGAGGAGTATGAG
GCATGGAAAGTTCGAAAGCTCAAGAAGGACAGAAAAGACAGAGAAGCGCATAAAAAGAAGAAAGCAGAAATTGCACACAT
GTGAAACCTGACTGAGCTTCAGGCAAATGGCAAAGTCATCACCAACAAAAGTGTT

Alignment

ORF - retro_itri_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.86 %
• Parental protein coverage: 72.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ALMKQPPIQSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAP-MESSDEEDEEFQFIKKAKEQEAEPE
          ALMKQ.PIQS.AGA..VR.E.GEISMEK.KVKRYVSGK.PDYAP.MESSDE.D.EFQFIKK..E.EA..E
Retrocopy ALMKQLPIQSKAGAILVRSENGEISMEKIKVKRYVSGKKPDYAP<MESSDEKDKEFQFIKKTQELEAQLE

Parental  EQEEDSSSDPRLRRLQNRISEDVEERLARHRKIVE-PEVVGESDSEVEGDAWRMERE-DTSEEEEEEIDD
          EQEEDSSSDP.LR.L.NR..EDVEERLA...KIV..P.VVGESDSEV.GDAW.ME.E...SEE.EE.ID.
Retrocopy EQEEDSSSDPWLRHL*NR--EDVEERLAQNPKIVY<PKVVGESDSEV-GDAWCMEQE<SSSEEKEENID-

Parental  EEIERRRGMMRQRAQERKN-EEMEVMEVEDEGRSGEESESESEYEEYTDSEDEMEPRLKP-VFIRKKDRV
          E..E...GMM.Q..QERKN.EEMEVMEV.DE..SGEESESESEYE.YT..EDEMEP...P...I.KKD..
Retrocopy EDVELHHGMMCQ*GQERKN>EEMEVMEV*DEEHSGEESESESEYEDYTYNEDEMEPCFTP<ILI*KKDQM

Parental  TVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRS-LAALDALNTDDENDEEEYEAW
          TVQ..EAEALKQKE.EQ.AK.MAE.RR.YTLKIVEEETKKELEENK.S.LAALD.L.TD.ENDEEEYEAW
Retrocopy TVQKCEAEALKQKEMEQGAKPMAEGRRNYTLKIVEEETKKELEENKCS<LAALDVLSTDSENDEEEYEAW

Parental  KVRELKRIKRDREDREALEKEKAEIERMRNLTEEERRAELRANGKV
          KVR.LK....DR.DREA..K.KAEI..M.NLTE.........N..V
Retrocopy KVRKLK---KDRKDREAHKKKKAEIAHM*NLTELQANGKVITNKSV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1105 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1105 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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,