RetrogeneDB ID: retro_itri_1118

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393379.1:1200547..1200879(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCFD2
• Ensembl ID: ENSSTOG00000003692
• Aliases: None
• Description: multiple coagulation factor deficiency 2 [Source:HGNC Symbol;Acc:18451]

Sequence

>retro_itri_1118
ATGCCAGGGCTGAGCAGCCTGGGCTTCGATAAGAACATGGTACATGACCAAGAGCATATCATGGAGCATCTGGAAGGTGT
CATCAACAAACCATAGGCGGAGATGTCCCCACAAGAACTGCAGCACCATTATTTCAAAATACACGATTATGATGGAAATA
ATTTACTTGATGGCTTAGAACTCTCTAGAGCCATCATGTCCATATGGAGGAAGAGAGTGAACAGGTGCCACTAATGAGCA
AAGAACTGATTTACATAATAGATGGTGTCTTGAGAGATGACAAGAACAATGATGGATACATTGACTAGGCTGAATTTGCA
AAATCACTGCAA

Alignment

ORF - retro_itri_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.74 %
• Parental protein coverage: 78.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPHPSSVGLDKNTVHDQEHIMEHLEGVINKPEAEMSPQELQHHYFKIHDYDGNNLLDGLELSTAITHVHK
          .P..SS.G.DKN.VHDQEHIMEHLEGVINKP.AEMSPQELQHHYFKIHDYDGNNLLDGLELS.AI.....
Retrocopy MPGLSSLGFDKNMVHDQEHIMEHLEGVINKP*AEMSPQELQHHYFKIHDYDGNNLLDGLELSRAIMSIWR

Parental  -EEESEQAPLMSEEELINIIDGVLRDDDKNNDGYIDYAEFAKSLQ
          .EE.SEQ.PLMS..ELI.IIDGVLR.DDKNNDGYID.AEFAKSLQ
Retrocopy <EE-SEQVPLMS-KELIYIIDGVLR-DDKNNDGYID*AEFAKSLQ

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_1118 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1118 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006097	2 retrocopies	retro_amel_720, retro_amel_906,
Bos taurus	ENSBTAG00000003358	1 retrocopy	retro_btau_629,
Canis familiaris	ENSCAFG00000032480	1 retrocopy	retro_cfam_797,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840, retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Myotis lucifugus	ENSMLUG00000004210	1 retrocopy	retro_mluc_2396,
Mustela putorius furo	ENSMPUG00000012043	1 retrocopy	retro_mputfur_885,
Sus scrofa	ENSSSCG00000021325	2 retrocopies	retro_sscr_1129, retro_sscr_422,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118 ,
Vicugna pacos	ENSVPAG00000010692	1 retrocopy	retro_vpac_368,