RetrogeneDB ID: retro_itri_1242

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393410.1:5230957..5231472(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD7
• Ensembl ID: ENSSTOG00000016345
• Aliases: None
• Description: StAR-related lipid transfer (START) domain containing 7 [Source:HGNC Symbol;Acc:18063]

Sequence

>retro_itri_1242
GTGATCAAGCTGGAGGTGACCAAGAGGGATGTGGTTAGTGGTTCTGAAGCTCTTCACTGGATAACCCATTTCTTTATCCA
TGTACTCTCAGTACGATGTGTATGTTCAATGGTACAGTGTGGATCCGGAAAATGTGATAGTGTTGGAGTCATGTGCTGTG
GAGCACCCCAGTGGTCCAGAAGCTCCAAAATTCATCAGGGTCAGATCATATGAATTCCAAATGGTTATCCATCTCCACAA
GTCACTTGATGAGAATAGCTTTGACTACTTGCTGACCTGCAGTGATAATCCCCAGACTGTGTTTCCTTGATACTGGGTTA
GTTGGATGGTTTCCAGCATGTGAGATTTCCTGGAGAAGCTGTGTGTGGCTACTCTGAAAGTCAAGAACACAAATCAAAGT
GAAGGACTACATCTCTGCAAAGCCTCTGAAAATGAGCAGGGAGGCCAAGGCCACTGCCCAGTCATCTGAGCAGAAGAACA
AGGACCATTGTAGTCCTACTCAGACTGAATATGCC

Alignment

ORF - retro_itri_1242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 63.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIKLEVIERDVVSGSEVLHWVTHF-PYP-MYSRDYVYVRRYSVDQENNVMVLVSRAVQHPSVPESPEFVR
          VIKLEV..RDVVSGSE.LHW.THF..YP.MYS...VYV..YSVD.EN.V.VL.S.AV.HPS.PE.P.F.R
Retrocopy VIKLEVTKRDVVSGSEALHWITHF<LYP<MYSQYDVYVQWYSVDPEN-VIVLESCAVEHPSGPEAPKFIR

Parental  VRSYESQMVIRPHKSFDENGFDYLLTYSDNPQTVFPRYCVSWMVSSGMPDFLEKLHTATL-KAKNMEIKV
          VRSYE.QMVI..HKS.DEN.FDYLLT.SDNPQTVFP.Y.VSWMVSS.M.DFLEKL..ATL.K.....IKV
Retrocopy VRSYEFQMVIHLHKSLDENSFDYLLTCSDNPQTVFP*YWVSWMVSS-M*DFLEKLCVATL>KSRT-QIKV

Parental  KDYIPAKPLEMSSEAKATAQSSERKNEGSCGPARIEYA
          KDYI.AKPL.MS.EAKATAQSSE.KN...C.P...EYA
Retrocopy KDYISAKPLKMSREAKATAQSSEQKNKDHCSPTQTEYA

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_1242 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1242 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001391	3 retrocopies	retro_chof_1979, retro_chof_2666, retro_chof_491,
Ictidomys tridecemlineatus	ENSSTOG00000016345	1 retrocopy	retro_itri_1242 ,