RetrogeneDB ID: retro_itri_5

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393384.1:552704..553187(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023414
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: AGPAT2
• Ensembl ID: ENSSTOG00000023422
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]

Sequence

>retro_itri_5
TCCAAGTACTGTATGCAGATCACCAAGCAGAAGCTGATGTTCCTCAAGCCGAGGGCCTCGTCCTGTTCCTTGGGGCCATC
TTTTCGTCAACCGAAGGCTCCAGTGCTGCCCCAACCCACCACAATAGCTAACTTGGGTGAGCGGAAGGTCAGGGAGAACC
TCAAAGTGTGGATCATCCCTAAGGGCATGTGCAATGAAAACAGGGACCTGCTGTCCTTCAAGAAATGTGCCTTTTACCTG
GCAATCCAACCCGTTCTACCTGTGGTATATTCTTCTTTTCCCTCCTTTTATAAACTCAAGACCAGGTTCTTCACCTCAGG
GACAATCAAGATGCAGGTGCTAGATGGAATCTCCACCAGCAGCCTCTCCGCGGTCAAGTTCATAGATACCTGCCATGCCA
TGAAGAGCACCTTACTCCATGTATCCACGATGCCTCAGGAGAACTGGCCAATGAAAGGCCTGATGTCCAGCCAGCCCAGT
AGC

Alignment

ORF - retro_itri_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.46 %
• Parental protein coverage: 72.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRCVQIAKRELLFLGPVGLIMYLGGVFFINRQRSSTALTVMADLGERMVEENLKVWIYPEGTRNDNGDLL
          K.C.QI.K..L.FL.P......LG..F...........T..A.LGER.V.ENLKVWI.P.G..N.N.DLL
Retrocopy KYCMQITKQKLMFLKPRASSCSLGPSFRQPKAPVLPQPTTIANLGERKVRENLKVWIIPKGMCNENRDLL

Parental  PFKKGAFHLAVQAQVPIVPVVYSSFSSFYNLKTKLFTSGTIKVQVLDAVPTSGLTVADVPKLMDTCYHAM
          .FKK.AF.LA.Q...P..PVVYSSF.SFY.LKT..FTSGTIK.QVLD...TS.L......K..DTC.HAM
Retrocopy SFKKCAFYLAIQ---PVLPVVYSSFPSFYKLKTRFFTSGTIKMQVLDGISTSSLSAV---KFIDTC-HAM

Parental  RSTFFHLSRTPQENGAIEG
          .ST..H.S..PQEN....G
Retrocopy KSTLLHVSTMPQENWPMKG

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_5 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_5 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003965	1 retrocopy	retro_amel_982,
Canis familiaris	ENSCAFG00000019569	1 retrocopy	retro_cfam_1838,
Equus caballus	ENSECAG00000010932	1 retrocopy	retro_ecab_825,
Felis catus	ENSFCAG00000011607	1 retrocopy	retro_fcat_1778,
Myotis lucifugus	ENSMLUG00000007348	2 retrocopies	retro_mluc_1291, retro_mluc_968,
Mustela putorius furo	ENSMPUG00000011249	1 retrocopy	retro_mputfur_1160,
Ochotona princeps	ENSOPRG00000003291	1 retrocopy	retro_opri_578,
Ictidomys tridecemlineatus	ENSSTOG00000023422	1 retrocopy	retro_itri_5 ,