RetrogeneDB ID: retro_itri_1047

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393363.1:2352537..2353236(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSSTOG00000001766
• Aliases: None
• Description: ariadne homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:690]

Sequence

>retro_itri_1047
CAATTTGTGCGGAAGGAAAACCTACTCTCTCTGGCCTGCCAGCACCAGTTTTGCCGCAGCTGCTGGGAGCAGCATTGCCC
AGTACTTGTCAAGGATGGTGTGGGTGTGGAAGTCTCTTGTATGGCTCAGGACTGTCCACTCTGTACACTAGAAGACTTTG
TGTTTCCATTGCTTCCCAATGAAGAATTGAAAGACAAATATAGGCGCTACCTTTTCAGGGATTATGTGGAGAGTCCTTAC
CAGCTCCAGCTGTGCCCTGGTGCAGACTGCCCCATGGTTATTCAGGTACAAGAGCTTACAGCTGGCCAAGTGCAGTGTAA
TCGGTGCAATGAGGTCTTCTGTTTCAAGTGTCATCAGATGTGTCATGCTCCCACAGACTGCACCACAATCCAGAAATGGC
TCACGAAATGTGCAGATGACTCTGAAATGGCCAACTACATTAGTGCTCACACTAAAGATTGTTCCAATTGCAACATCTGC
ATTGAGAAGAATGGAGGCTGCAATCATATGCGATGCTCCTAATGTAAACACGACTTCTGCTGGATGTGTCTAAGAGATTG
GAAGACTCATGGCAGTGAGTACTATGAGTACAGTCAGTACAAAGAGAACAAACCAGAGAATCCTGACATTGTCAACCAGA
GTCAGCAAGCCCAGGCCAGGGAGGCCCTCAAGAAGTACTTATTCTATTTTGAGAGGTGG

Alignment

ORF - retro_itri_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.84 %
• Parental protein coverage: 54.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELKDKYRRY
          QFVRKENLLSLACQHQFCRSCWEQHC.VLVKDGVGV.VSCMAQDCPL.T.EDFVFPLLPNEELKDKYRRY
Retrocopy QFVRKENLLSLACQHQFCRSCWEQHCPVLVKDGVGVEVSCMAQDCPLCTLEDFVFPLLPNEELKDKYRRY

Parental  LFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADD
          LFRDYVES.YQLQLCPGADCPMVI.VQE..A..VQCNRCNEVFCFKC.QM.HAPTDC.TI.KWLTKCADD
Retrocopy LFRDYVESPYQLQLCPGADCPMVIQVQELTAGQVQCNRCNEVFCFKCHQMCHAPTDCTTIQKWLTKCADD

Parental  SETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKEN----PDI
          SE.ANYISAHTKDC..CNICIEKNGGCNHM.CS.CKHDFCWMCL.DWKTHGSEYYE.S.YKEN....PDI
Retrocopy SEMANYISAHTKDCSNCNICIEKNGGCNHMRCS*CKHDFCWMCLRDWKTHGSEYYEYSQYKENKPENPDI

Parental  VNQSQQAQAREALKKYLFYFERW
          VNQSQQAQAREALKKYLFYFERW
Retrocopy VNQSQQAQAREALKKYLFYFERW

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_1047 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1047 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013035	1 retrocopy	retro_amel_1021,
Callithrix jacchus	ENSCJAG00000003305	1 retrocopy	retro_cjac_1106,
Homo sapiens	ENSG00000177479	1 retrocopy	retro_hsap_1876,
Gorilla gorilla	ENSGGOG00000017134	1 retrocopy	retro_ggor_1373,
Myotis lucifugus	ENSMLUG00000013946	1 retrocopy	retro_mluc_1869,
Mustela putorius furo	ENSMPUG00000014344	1 retrocopy	retro_mputfur_610,
Mus musculus	ENSMUSG00000064145	1 retrocopy	retro_mmus_795,
Nomascus leucogenys	ENSNLEG00000006710	1 retrocopy	retro_nleu_1228,
Oryctolagus cuniculus	ENSOCUG00000017699	1 retrocopy	retro_ocun_1838,
Pongo abelii	ENSPPYG00000013890	1 retrocopy	retro_pabe_1557,
Pan troglodytes	ENSPTRG00000014902	1 retrocopy	retro_ptro_1259,
Ictidomys tridecemlineatus	ENSSTOG00000001766	1 retrocopy	retro_itri_1047 ,