RetrogeneDB ID: retro_itri_383

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393288.1:9065435..9065837(+)
• Located in intron of: ENSSTOG00000009855

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1D
• Ensembl ID: ENSSTOG00000027710
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D [Source:HGNC Symbol;Acc:13527]

Sequence

>retro_itri_383
CATGAAGAAACTGACAGTTATGAACTAACTGGTTTAACCAGAGGTGGGGAACAGTTGGCTATATTAAAGAGGAATTATGC
CAAAGCAGTGGAACTACTGGTGGAACTAGCTTCACTACAGACTTCCTTTGTGATTCTGGATGAAGCTATTACGATAACTA
ACAGGTGTGTGAATGCCATTGCACATGTCATCATTCCACGGATTGAACACACTCTTGCTCATATCATCACAGAGCTGGAC
GAAAGAGAGTGAGAAGAGTTCTATAGGTTAAAGAAAATACAGGAGAAGAAGATTCTCAAGTAAAAATGTGAGAAGGATTT
GGAGCAACGGAAAGCAGCTGGAGAGGTGATGGAGCCTGCTAACCTTCTTGCTGAGGAGAAGGACGAGGATCTTCTGTTTG
AA

Alignment

ORF - retro_itri_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.85 %
• Parental protein coverage: 56.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HRILDFYKWSSLVKRQELSLSSTKXNSVSSMEISHKFCFLKTSFVTLDEAIKITNRRVNAIEHVIIPRIE
          H...D.Y....L....E..L...K.N.....E.......L.TSFV.LDEAI.ITNR.VNAI.HVIIPRIE
Retrocopy HEETDSYELTGLTRGGE-QLAILKRNYAKAVELLVELASLQTSFVILDEAITITNRCVNAIAHVIIPRIE

Parental  RTLAYIITELDEREREEFYRLKKIQEKKKILKEKCEKDLEQRRAAGEVMEPANLLAEEKDEDLLFE
          .TLA.IITELDERE.EEFYRLKKIQEKK.ILK.KCEKDLEQR.AAGEVMEPANLLAEEKDEDLLFE
Retrocopy HTLAHIITELDERE*EEFYRLKKIQEKK-ILK*KCEKDLEQRKAAGEVMEPANLLAEEKDEDLLFE

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_383 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_383 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 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383 ,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,