RetrogeneDB ID: retro_itri_405

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:4979786..4980243(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSSTOG00000003825
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:HGNC Symbol;Acc:30246]

Sequence

>retro_itri_405
ATAGTGACAGACAATGGAGCCTTTATCAATATCCCAGTCTGTTAGAAGCAAAGTCTGGCCCATCAAACTCACATGTCATC
CTGTCAGGTGGATAAGCCCTCTGAGATAGTAGATGTCAGAGGCAAAATGTGGGTGAAACTTACTGGCTGAGAGATGAAAA
ATGATAGAATAAAAGTACCCCTGTACATCAAACTTGTCAACCAAGGGACTAGGGTAGACCTTGATCCCCAAAACATGTCA
TTGAGCAAGAAGAGGGACAAAGGTGGTCCTTCCAGGATTACACTGGGCAGAAAATCACGCTTGAGGCTGTCCTGAACACT
ACTGGCAAGAAGTGTGGCTATAAAGGCCACTTTGAGAAAGATTATTTTTGGCAACTATGTAGGACCAAATATTCTCTGAT
ACCTGATGAGGAAGAGAAGAAAGAAGACACAAAGTGGACGAATTTGAGAAGCCTGAT

Alignment

ORF - retro_itri_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 70.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGT
          .VTD.GAFI.IP.C.KQ.L.H.THMSSC.VDKPSEIVDV..K.WVKL.G.EMKNDRIKV.L..K.VNQGT
Retrocopy IVTDNGAFINIPVC*KQSLAHQTHMSSCQVDKPSEIVDVRGKMWVKLTG*EMKNDRIKVPLYIKLVNQGT

Parental  GKDLDPNNV-IIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKGHFAKDCFMQPGGTKYSLIPDEEE
          ..DLDP.N...IEQEE..R.SFQDYTGQKITLEAVLNTT.KKCG.KGHF.KD.F.Q...TKYSLIPDEEE
Retrocopy RVDLDPQNM<VIEQEEGQRWSFQDYTGQKITLEAVLNTTGKKCGYKGHFEKDYFWQLCRTKYSLIPDEEE

Parental  EKEETKSA-EFEKPD
          .KE.TK...EFEKPD
Retrocopy KKEDTKWT<EFEKPD

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_405 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_405 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405 ,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,