RetrogeneDB ID: retro_itri_974

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393353.1:8050366..8050744(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF11
• Ensembl ID: ENSSTOG00000020072
• Aliases: None
• Description: ring finger protein 11 [Source:HGNC Symbol;Acc:10056]

Sequence

>retro_itri_974
GACCGCGCCAGCTTTGGCGAGGAGACAGAGCAGGATCAGGAGCCGCTGCATCAGGAACAAGTTCCAGTTCCAATGTATCG
TCCAACACCCGACTCCGCTAGCAACTCCGAAGAGGAACAAATTAGGACAGCTCAAAGAATAGGCCTTACACAGCATCTGC
CTAAGGGAGCTTATGACCCTGGCAGAGATGGGTCAGGAAAAAAGCTCGGGAGTGTGTGATCTCTGTGATGGACTCTTGTT
TATGGGGACTCAATTCGATTTCTGCCATGCATGCACATCTATCACCTGGGCTGCTCAGGTGACTGGTTGATGAGCTCCTC
CACGTGCCCATCCTGCATGGAGCCAGTTGATGCAGCACTGCTTTTATCCTATGAGACT

Alignment

ORF - retro_itri_974 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.9 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRASFGEGTEPDQEPPPPYQEQVPVPVYHPTPSQTRLATQLTEEEQIRIAQRIGLIQHLPKGVYDPGRDG
          DRASFGE.TE.DQEP....QEQ..VPV..P....T.......EEEQIR.AQRIGL.QHLPKG.YDPGRDG
Retrocopy DRASFGEETEQDQEPL--HQEQ--VPV--PMYRPTPDSASNSEEEQIRTAQRIGLTQHLPKGAYDPGRDG

Parental  SEKKI-RECVICMMD-FVYGDPIRFLPCMHIYHLDCIDDWLMRSFTCPSCMEPVDVALLSSYET
          S.KK..RECVI..MD..VYGD.IRFLPCMHIYHL.C..DWLM.S.TCPSCMEPVD.ALL.SYET
Retrocopy SGKKL<RECVISVMD>LVYGDSIRFLPCMHIYHLGCSGDWLMSSSTCPSCMEPVDAALLLSYET

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_974 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_974 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000006072	1 retrocopy	retro_etel_873,
Homo sapiens	ENSG00000123091	1 retrocopy	retro_hsap_3925,
Gorilla gorilla	ENSGGOG00000004919	1 retrocopy	retro_ggor_2641,
Myotis lucifugus	ENSMLUG00000004439	1 retrocopy	retro_mluc_145,
Otolemur garnettii	ENSOGAG00000011682	1 retrocopy	retro_ogar_2003,
Pongo abelii	ENSPPYG00000001361	1 retrocopy	retro_pabe_3241,
Pan troglodytes	ENSPTRG00000041089	1 retrocopy	retro_ptro_2669,
Ictidomys tridecemlineatus	ENSSTOG00000020072	4 retrocopies	retro_itri_1747, retro_itri_1886, retro_itri_633, retro_itri_974 ,
Tursiops truncatus	ENSTTRG00000010211	1 retrocopy	retro_ttru_1644,