RetrogeneDB ID: retro_itri_311

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:15164671..15165036(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD7
• Ensembl ID: ENSSTOG00000006640
• Aliases: None
• Description: COMM domain containing 7 [Source:HGNC Symbol;Acc:16223]

Sequence

>retro_itri_311
TTTTTCTACTTCTTGAGCTCCAAAGCAATGTAAAGATTTTTGGCACAGCTGTCTGAATTTGGAATTACCAATCAGATCAG
TATTGGCCCCCTAACAAGCATCAAGAAAAGCCTTCTCCCTGGTTCCAAATGGCTCCTTAAAGAAGAGTCTCAACAGCTGA
GCAGATTTACATGGGTTTCCTTAATGCTAGGTTTTAGGGAGGAGAAAGTCCCTTATGTGTTGAAAAGTGGAAACAGAATG
CCCCTATACTTTTTGAATGGTCCATCAGTCAGATCCTGATGATTAATCAGTTTATTAATAGGGAGTGGAAGTTTGGAGTG
ACATCTGGGAATAGCAAATTGGACAAAGTGGGAAGAATTTTTTTG

Alignment

ORF - retro_itri_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.0 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FHFLIEPKEVERFLAQLSEFATTNQISLGPLRSIVKSLL-LVPNGALKRSL-TAEQVRADFLT-LGLSEE
          F......K...RFLAQLSEF..TNQIS.GPL.SI.KSLL.LVPNG.LK.SL.TAEQ....FL..LG..EE
Retrocopy FFYFLSSKAM*RFLAQLSEFGITNQISIGPLTSIKKSLL>LVPNGSLKKSL>TAEQIYMGFLN>LGFREE

Parental  KATYFS-EKWKQNAPTLAQWALGQTLMINQLIDMEWKFGVTSGSSELEKVGSIFL
          K..Y...EKWKQNAP.L..W...Q.LMINQ.I..EWKFGVTSG.S.L.KVG.IFL
Retrocopy KVPYVL<EKWKQNAPILFEWSISQILMINQFINREWKFGVTSGNSKLDKVGRIFL

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_311 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_311 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008561	2 retrocopies	retro_chof_1254, retro_chof_345,
Loxodonta africana	ENSLAFG00000008789	1 retrocopy	retro_lafr_1194,
Macropus eugenii	ENSMEUG00000010627	1 retrocopy	retro_meug_1062,
Monodelphis domestica	ENSMODG00000019450	3 retrocopies	retro_mdom_1047, retro_mdom_313, retro_mdom_890,
Sarcophilus harrisii	ENSSHAG00000006762	1 retrocopy	retro_shar_142,
Ictidomys tridecemlineatus	ENSSTOG00000006640	1 retrocopy	retro_itri_311 ,