RetrogeneDB ID: retro_itri_288

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393282.1:29599036..29599559(+)
• Located in intron of: ENSSTOG00000012208

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSSTOG00000015507
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_itri_288
CCTGCTTCTGTGTTGCTGCTACTGTTTCCTCTTATCACCCAACATGAGACTATCAGGAAAAAGAAATTGAAGAACTGAAG
GACAAGAAGGTAGTCCTAAAATATACTTCATGAAACAGACCATCAAGAACTCCTGTGGTAAGATCAGGCTGATACATGCA
ATGGCAAGTAATCAAAACAGACTTTAGTTTGAGGATGAATCATTCCTGATATAATTTGTTTCTGAAATGAAGATGTCTCA
TGAAGAGATAGTGAAATGCTTTGAAAACGATTAGGTCATTCCAGCATCCCATCTTGCCATGACACAGGAAGGCCATTGTA
ATGATAATGATAGTCAATTTTCATTTCATTCTGTTTATCAACATGGATGGCCACCTCTATGAACTTGATGGGTCAGTGCC
TTTGAACCATGGCACCAGTTCAGAGAGCTCACTACTTGAGGATGCTTTTGAGGTCTGCAGAGACTTCATTGAGCATGAGC
AAGGGGAAGTCAGCTTCTCTGCTGAGCCCTCTGTAAGGTAGCC

Alignment

ORF - retro_itri_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.93 %
• Parental protein coverage: 80.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PACALLLLFPLTAQHENFRKK-QIEELK-GQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLEFEDGS
          PA..LLLLFPL..QHE..RKK..IEELK.GQE.SPK.YFMKQTI.NSCG.I.LIHA.A.NQ..L.FED.S
Retrocopy PASVLLLLFPLITQHETIRKK<EIEELK<GQEGSPKIYFMKQTIKNSCGKIRLIHAMASNQNRL*FEDES

Parental  VLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHF-ILFNNVDGHLYELDGRMPF
          .L..F.SE..KMS.E...KCFE....I.A.H.A..QEG.C..D....F.F.ILF.N.DGHLYELDG....
Retrocopy FLI*FVSEM-KMSHEEIVKCFEND*VIPASHLAMTQEGHCN-DNDSQFSF>ILFINMDGHLYELDGSV--

Parental  PVNHGTSSEGSLLQDAAKVCREFTEREQGEVRFSAV-ALCKAA
          P.NHGTSSE.SLL.DA..VCR.F.E.EQGEV.FSA..ALCK.A
Retrocopy PLNHGTSSESSLLEDAFEVCRDFIEHEQGEVSFSAE<ALCKVA

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_288 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_288 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003295	1 retrocopy	retro_chof_1737,
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Felis catus	ENSFCAG00000025457	1 retrocopy	retro_fcat_1321,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Ictidomys tridecemlineatus	ENSSTOG00000015507	1 retrocopy	retro_itri_288 ,
Tupaia belangeri	ENSTBEG00000011438	1 retrocopy	retro_tbel_306,
Tursiops truncatus	ENSTTRG00000012095	1 retrocopy	retro_ttru_1370,