RetrogeneDB ID: retro_itri_1494

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393509.1:1830165..1830886(-)
• Located in intron of: None

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_1494
GAGCCTCAACCTAAGCCAGTCTTCATTCAAAAGTAGGACTGAATGACAGTTCAAAAACATGAGGCTGAAGCATTGAAACA
GGAAGAGATGGAGCAGGAAGCAAAATGCATGGCTGAAGGAAAGTGAATGTACACATTCTAGATTGTAAAAGAGGAGACCA
AAAAAGACCTGGAGGAGAACAGCATTCCCTGGCTGCAGTGGATGCACTCAATACTGATGATGAAAAGGATGAGGAGAAAT
ATGAGGCATGCAAAAGTTTGGGAATGAAAAAGAATCAAGAGGGAGAAAAGAGCGAGAAACACTTGAAAAAAAGACAGGAG
AAATTGAACCCATGAAAAACTTGACTGAGGAAGAGAGGCAAGCTGAACTTTAGGCAAATGGCAAAGTCATTACTAATAAA
GCTGTTAAGGGCAAATACAAGTTGTTACAAGTACTGTCACCTGGGTTCCTTTTTCATGGAAAAGGATGAGAGTGTATTCA
AGAGAGATTTCAATGCATCTACCTTGGAGGATCTTTTCAACAAAAACATTCTTCCTAAAGTCACACAGGTTGAGAACTAT
TGATGTCCTGGTCATAACAAATACACCCACCATATAGATCAAGACACCCTCTCCTTTGACTCAACATGGACCCAGGAGAG
TGCCCAGAACACAAAGTTCTTTAAACCAAAGGCATCAGAGTATGTACTGTATTTGAGCAAGCATCTGCCAAGAAGCATAA
A

Alignment

ORF - retro_itri_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 55.13 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EPRLKPVFIRKKDRVTVQEREAEALKQKELEQEAKRMAEERRKYTLKIVEEETKKELEEN-KRSLAALDA
          EP..KPVFI.K.D..TVQ..EAEALKQ.E.EQEAK.MAE....YT..IV.EETKK.LEEN...SLAA.DA
Retrocopy EPQPKPVFIQK*D*MTVQKHEAEALKQEEMEQEAKCMAEGK*MYTF*IVKEETKKDLEEN<QHSLAAVDA

Parental  LNTDDENDEEEYEAWKVRELKRIK-RDREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKG
          LNTDDE.DEE.YEA.K....K....R.R..RE.LEK...EIE.M.NLTEEER.AEL.ANGKVITNKAVKG
Retrocopy LNTDDEKDEEKYEACKSLGMKKNQ<RGRKERETLEKKTGEIEPMKNLTEEERQAEL*ANGKVITNKAVKG

Parental  KYKFLQKYYHRGAFFMDEDEEVYKRDFSAPTLEDHFNK-TILPKVMQVKNFGRSGRTKYTHLVDQDTTSF
          KYK.LQ.....G..F.....E.....F....L...F....ILPKV.QV.N....G..KYTH..DQDT.SF
Retrocopy KYKLLQ-VLSPGFLFHGKG*ECIQERFQCIYLGGSFQQ>NILPKVTQVENY*CPGHNKYTHHIDQDTLSF

Parental  DSAWGQESAQNTKFFKQKAA-GVRDVFERPSAKKRK
          DS.W.QESAQNTKFFK.KA...V..VFE..SAKK.K
Retrocopy DSTWTQESAQNTKFFKPKAS<RVCTVFEQASAKKHK

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_1494 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1494 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.

---

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,