RetrogeneDB ID: retro_itri_158

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393629.1:1044647..1045598(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000014071
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FOXR1
• Ensembl ID: ENSSTOG00000014321
• Aliases: None
• Description: forkhead box R1 [Source:HGNC Symbol;Acc:29980]

Sequence

>retro_itri_158
ATGGACCTAAAGCTAAAAAATCCTGACTTCTGGTACAGTCTTCATGGACATGTTCCAGGACTTCTGGACTGGGACATGGG
GAATGAGTTCTTCTTGCCTTGTACCACAGACCAGAGCCCTTTAGCTGAGCAGAACCTTGCTAAATACAAAATACGAGTAA
TGAAGCCCCCAGAAGTACCCCAGGAGTGGAAACTTGGTCCTGATGAAGATGCTCCTCAGTCTGAACCCAACTTGTGGATG
TGGGTGAACCCAAACATTGTGTGCCCTCTCAGCAGCCAGGAGGCCCTAAAGCCCAATAGTAAGGATCTGACAAGCATGGC
TTCTTCCCCTCAGGCACCCACAAAAGATGAAGAGTCTAACTTCTCAGAGGCTCAGGGAGTGTTGGAGTCCCTGCCACTTT
CCTCCAGTGATCAGTCTCCCCAACAGAAGCACCTCTTCTCTTCCCCAAGTGACTGTGAGCTCACAGAAGAGGAAGCTGAG
GAACAAGAGGACAAGTCTTCTGAGGCCCTCATGGCCCTTAACAAAAGGGACTGCTTCCAGAAGCCAAAGCTGTGGCAAGC
TAACAACCAGGAAAGGAAATCCTGGCCACGGCCCCCACTCAATTATAGCCATCTCATTGCCCTAGCATTAAGAAACAGCC
CTCCTTGTGGTCTTAATGTGCAACAGATCTACAATTTCACTCGACAGCATTTCCCCTTTTTCTGGACAGCTCCAGATGGC
TGGAAAAACACCATTCGCCACAACCTCTGCTTCCTAGGCAGCTTTGAAAAGGTGCCAGTCACTGTTCAGGATGAGGCTGA
TGCAAAACCTCGCTCTTGCCTCTGGAGGCTCACCGAGGAGGGACACCGCCACTTTAAGGAGGATACCCGTCTCTTAGCCT
CTGCTAGAAGAGAGAGCATCCAACAGTGCATGAGCCAACCAGATTTGATGTCCTCCCTCTTTGACCTTTGA

Alignment

ORF - retro_itri_158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNESFLAFTTAHLPLTEQNLARYKLRIVEPPKLPLGKKPNADEDGPDIEPNLWMWVNPNVVYPPGKLEV
          MGNE.FL..TT...PL.EQNLA.YK.R...PP..P...K...DED.P..EPNLWMWVNPN.V.P....E.
Retrocopy MGNEFFLPCTTDQSPLAEQNLAKYKIRVMKPPEVPQEWKLGPDEDAPQSEPNLWMWVNPNIVCPLSSQEA

Parental  TESKKGEDLMSEPPSPQAPPKEEDASCCSEAARAESSLHSSSEQSPPRKQFASSPSNWELPEEEEAKDQD
          .......DL.S...SPQAP.K.E...........ES...SSS.QSP..K...SSPS..EL.EEE.A..Q.
Retrocopy LKPNS-KDLTSMASSPQAPTKDEESNFSEAQGVLESLPLSSSDQSPQQKHLFSSPSDCELTEEE-AEEQE

Parental  DSSSVALPSPHTRAPLQSRRLRQAISPEGRLWSRPPLNYFHLIALALRNSPPCGLNVQQIYSFTRQHFPF
          D.SS.AL.....R...Q...L.QA...E...W.RPPLNY.HLIALALRNSPPCGLNVQQIY.FTRQHFPF
Retrocopy DKSSEALMALNKRDCFQKPKLWQANNQERKSWPRPPLNYSHLIALALRNSPPCGLNVQQIYNFTRQHFPF

Parental  FRTAPEGWKNTVRHNLCFRDSFEKVPVSMQGEASTRPRSCLWKLTEEGHRRFAEEARALASTRLESIQQC
          F.TAP.GWKNT.RHNLCF..SFEKVPV..Q.EA...PRSCLW.LTEEGHR.F.E..R.LAS.R.ESIQQC
Retrocopy FWTAPDGWKNTIRHNLCFLGSFEKVPVTVQDEADAKPRSCLWRLTEEGHRHFKEDTRLLASARRESIQQC

Parental  MSQPDVMPFLFDL
          MSQPD.M..LFDL
Retrocopy MSQPDLMSSLFDL

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_158 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_158 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000053	1 retrocopy	retro_amel_39,
Bos taurus	ENSBTAG00000014606	1 retrocopy	retro_btau_189,
Canis familiaris	ENSCAFG00000012417	1 retrocopy	retro_cfam_209,
Callithrix jacchus	ENSCJAG00000013656	1 retrocopy	retro_cjac_4066,
Dasypus novemcinctus	ENSDNOG00000009414	1 retrocopy	retro_dnov_22,
Dipodomys ordii	ENSDORG00000001960	1 retrocopy	retro_dord_651,
Homo sapiens	ENSG00000176302	1 retrocopy	retro_hsap_72,
Microcebus murinus	ENSMICG00000002680	1 retrocopy	retro_mmur_38,
Macaca mulatta	ENSMMUG00000022722	1 retrocopy	retro_mmul_125,
Mustela putorius furo	ENSMPUG00000004890	1 retrocopy	retro_mputfur_161,
Nomascus leucogenys	ENSNLEG00000007376	1 retrocopy	retro_nleu_50,
Otolemur garnettii	ENSOGAG00000007258	1 retrocopy	retro_ogar_296,
Procavia capensis	ENSPCAG00000010132	1 retrocopy	retro_pcap_12,
Pongo abelii	ENSPPYG00000003947	1 retrocopy	retro_pabe_69,
Pan troglodytes	ENSPTRG00000004358	1 retrocopy	retro_ptro_94,
Sorex araneus	ENSSARG00000011319	1 retrocopy	retro_sara_38,
Sus scrofa	ENSSSCG00000015101	1 retrocopy	retro_sscr_36,
Ictidomys tridecemlineatus	ENSSTOG00000014321	1 retrocopy	retro_itri_158 ,