RetrogeneDB ID: retro_itri_1045

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393362.1:5615008..5615629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C4orf17
• Ensembl ID: ENSSTOG00000013616
• Aliases: None
• Description: chromosome 4 open reading frame 17 [Source:HGNC Symbol;Acc:25274]

Sequence

>retro_itri_1045
TTGAATAACATTCTTATTGTACTGTGAATGACCGTGAGACTGAACTCAGAACATAGTGAGGCATTAGCCAGTTTAACCCC
TTAGAGAAGGATGAGATACCCCTTACAAAATGTATGACCCACCCCAACAGAGCAGCTCTGGAGAGTCCTGTTAGAGGATT
GTCACTAGCCCCAAACAATGTCAAAATGCCCCCTTTGACCTCGTTTAGAGCCCAGCAGGAAAATCAGAGTGCTTCAAAAT
TCCCAGTGAGAATCTCTTCTTAATTAAAAAGGAAGAAATCAAGGCTAAAAATCCACCATCACCTCCAACTTCATCCTCTA
CTGCTGGCTCCCATTCTTCAGAGGGGATGAGAACCAAAACTGACATCAAAGAGTACACCATTTGCCTACCAAACTATCCA
GATCAAGAAAGAAAGATCCTATCAAAGCTCGGTGGCATTTTATGCACTGATTCCCTTGTAGAAGTTACACAGCGGCTGCT
TCATGCAAAGAAAAGGAAAAATAAGGGGTCTCAGCTTTGATTCATTCTGAGTGGGCTGAGATGAACTTGTTGATCCTCCC
CAGAAGAAACACCTCTGTGGAACCAGCAGCCGAGACTGGGAAGCCACTCCCAATCAAATCA

Alignment

ORF - retro_itri_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LNNIPI-CTVNDDELALGALYGVSQFDQLEKDEIPFAKCNYPPSPAAPESPVREVSPAQSRV-KMPPRPH
          LNNI.I.CTVND.E..L....G.SQF..LEKDEIP..KC...P..AA.ESPVR..S.A...V.K.P..P.
Retrocopy LNNILI<CTVNDRETELRT**GISQFNPLEKDEIPLTKCMTHPNRAALESPVRGLSLAPNNV>KCPL*PR

Parental  SE-PCRKFNECFKTSSENPLVIKKEEIKVKKSPSPPNACYTAGSCSSEAMSTKADVKENTVCIPNYLDQE
          .E.P..K..ECFK..SEN...IKKEEIK.K..PSPP....TAGS.SSE.M.TK.D.KE.T.C.PNY.DQE
Retrocopy LE>PAGK-SECFKIPSENLFLIKKEEIKAKNPPSPPTSSSTAGSHSSEGMRTKTDIKEYTICLPNYPDQE

Parental  IKILAKLCDILHTDSLAEVTQWLLHA-STKEKEWISALIHSELAEIHLLSRHRRNTPVEPAGETGKPSAV
          .KIL.KL..IL.TDSL.EVTQ.LLHA...KEK...SALIHSE.AE..LL...RRNT.VEPA.ETGKP...
Retrocopy RKILSKLGGILCTDSLVEVTQRLLHA<KEKEK*GVSALIHSEWAEMNLLILPRRNTSVEPAAETGKPLPI

Parental  KS
          KS
Retrocopy KS

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_1045 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1045 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013616	1 retrocopy	retro_itri_1045 ,