RetrogeneDB ID: retro_itri_1568

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393544.1:229078..229750(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL16
• Ensembl ID: ENSSTOG00000011876
• Aliases: None
• Description: methyltransferase like 16 [Source:HGNC Symbol;Acc:28484]

Sequence

>retro_itri_1568
GAATTAGAATTTGTTAAATGATCATCTATCACAGTTTACAGCTTTAAAAAAGGCTAAGGTGGTAGAGCTGTATGCTGGGA
AAGAAATGCAGCCTGGCTCCACTGAAGGAAGAACTTCGCATCCAAGGGGTTCCCAAAGTTACCTTCACTGAGTTTCGTCA
AGGTTTTGTCAATGAGGTAGGCCTTAGCTTGGAGTTTTTATGATGATATCACAGTACCATTCCCATCACGTAAGCGAAAA
AGTAGAGAAGCCAAGAAAACCCATGACATTGTGGTGTTGGAGTCTGTGATGAAAGACTTATTCCTCGAAGAATCATCCTT
GGGCCCTGAGACATGGAGGGCATAGTGGTCTTAACAACATGGATAGAAAAAATTCTCACTGATTTAAAGGTCTAGCAAAA
ATGAGTTCCCTGTAGAAAACAGGGAGTTAGTCTTTCCCCGAAAGCCACAGAAAACTCCTGAATTCATTTAAGGCGAAAGA
ACAGAAAGCCAGTAAGACAACTGAGAGAAGTGCCTGGAGCTCCTGAGGATGTCATACAGGCCTTGGAGGAGAGAAAAGCT
ATCCCCAGAGAATGGGGCAGTAGCCAGAATTTGGCCCCAAGCCCCCAGGAGGGTACCCTGAGGGGTCTGCTCTGCAGAGG
GCGAGTCTGCCACTATTGGGGGCCACTGCCCA

Alignment

ORF - retro_itri_1568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 65.89 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ELEFVK-RIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTFTEFCQG-RTMRWALAWSFYD
          ELEFVK..II..SLQL.KRLRW.SCMLGKKCSLAPLKEELRIQGVPKVTFTEF.QG...MR.ALAWSFYD
Retrocopy ELEFVK<MIIYHSLQL*KRLRW*SCMLGKKCSLAPLKEELRIQGVPKVTFTEFRQG>LSMR*ALAWSFYD

Parental  DVTVPLPPSKRRK-LEKSRKPITF-VVLESVMKELSLKASSLGSEK-VEGIVVVTTWIEKILTDLKVQHK
          D.TVP.P.S..RK..EK.RKP.T..VVLESVMK.L.L..SSLG.E...EGIVV.TTWIEKILTDLKV..K
Retrocopy DITVPFP-SRKRK>VEKPRKPMTL<VVLESVMKDLFLEESSLGPET<MEGIVVLTTWIEKILTDLKV*QK

Parental  RVPCGKEEASLFLTAIENSWIHLRRKKRKQVRQLREVPRAPEDVIQALEERKAIPRESGNSQDVALSPQE
          .VPC.K...SL...A.ENS.IHLRRK.RK.VRQLREVP.APEDVIQALEERKAIPRE.G.SQ..A.SPQE
Retrocopy *VPCRKQGVSLSPKATENS*IHLRRKNRKPVRQLREVPGAPEDVIQALEERKAIPREWGSSQNLAPSPQE

Parental  GTLCGF-ALQ-EGESATVGGYCP
          GTL.G..ALQ.EGESAT.GG.CP
Retrocopy GTLRGL<ALQ<EGESATIGGHCP

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_1568 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1568 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017440	2 retrocopies	retro_btau_1159, retro_btau_1533,
Myotis lucifugus	ENSMLUG00000003531	2 retrocopies	retro_mluc_1130, retro_mluc_1625,
Monodelphis domestica	ENSMODG00000010765	2 retrocopies	retro_mdom_305, retro_mdom_339,
Otolemur garnettii	ENSOGAG00000004504	1 retrocopy	retro_ogar_491,
Ictidomys tridecemlineatus	ENSSTOG00000011876	1 retrocopy	retro_itri_1568 ,