RetrogeneDB ID: retro_itri_1390

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393470.1:3550394..3550912(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL5C
• Ensembl ID: ENSSTOG00000011104
• Aliases: None
• Description: ADP-ribosylation factor-like 5C [Source:HGNC Symbol;Acc:31111]

Sequence

>retro_itri_1390
ATGGGAATTCTCTTCACCAGGATATGGAGGCAATTCAATCACCAGGGTCACAAAATTATCATTGTAGTGTTGGACAATGC
AGGAAAAACTACCATCTTCATAATTTTCTATGAATGAAATTGTACATACATTCTCTTACAATAGAAAGTAAGATAGAAGA
GATAGTTATTAATGATGTACATTTGCTAATGTGGGATATTGGTGGCCAAGAATTTCTTTGTTTTTCTTTGAATACTTTTA
ATAACATGGACTTCATAATAGTAGTTGTGGACAGTACAGACAGAGATTTCTGTAACTAAAGAAGAACTCTACAAACTATT
AGTGCATAGGATGTAAGAAAAACTGGATTACTTATTTTTGCTAAAAAACGTGAATGCATGACTGTTGTGGAAATCTACCA
TTTTTTGAAGCTAGCTTCTTTTAAAGATCATCAGTCACCTATCCAGGCATGCTATGCTCTTACCGGTGAGGGATTATGCC
AAGGTCTTGAATGGAAAATGTCACAATTTAGGATTAAA

Alignment

ORF - retro_itri_1390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.63 %
• Parental protein coverage: 98.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGQLIAKLMGIFGNQEHKVIIVGLDNAGKTTI-LYQFL-TNEVVHTCP-TIGSNVEEIVLRKTHFLMWDI
          MG.L.......F..Q.HK.IIV.LDNAGKTTI.L..FL..NE.VHT...TI.S..EEIV....H.LMWDI
Retrocopy MGILFTRIWRQFNHQGHKIIIVVLDNAGKTTI<LHNFL<MNEIVHTFS>TIESKIEEIVINDVHLLMWDI

Parental  GGQEALRSTWSTYYSNTEFVILVIDSTDRDR-LPTTREELYKMLAHEA-LRDASVLIFANKQDVKDSMTT
          GGQE.L.....T...N..F.I.V.DST..DR....T.EELYK.L.H....R....LIFA.K......MT.
Retrocopy GGQEFLCFSLNTF-NNMDFIIVVVDST--DR>ISVTKEELYKLLVHRM<VRKTGLLIFAKK---RECMTV

Parental  VEISQFLTLSAIRDHPWHIQGCCALTGEGLPAGLQWMQSQATAK
          VEI..FL.L....DH...IQ.C.ALTGEGL..GL.W..SQ...K
Retrocopy VEIYHFLKLASFKDHQSPIQACYALTGEGLCQGLEWKMSQFRIK

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_1390 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1390 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000030149	1 retrocopy	retro_mluc_1488,
Ictidomys tridecemlineatus	ENSSTOG00000011104	1 retrocopy	retro_itri_1390 ,
Ictidomys tridecemlineatus	ENSSTOG00000016022	2 retrocopies	retro_itri_1000, retro_itri_348,
Ictidomys tridecemlineatus	ENSSTOG00000016326	1 retrocopy	retro_itri_62,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580,