RetrogeneDB ID: retro_itri_1613

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393574.1:171997..172519(+)
• Located in intron of: ENSSTOG00000000925

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRKB
• Ensembl ID: ENSSTOG00000016406
• Aliases: None
• Description: TP53RK binding protein [Source:HGNC Symbol;Acc:24259]

Sequence

>retro_itri_1613
ATGCAGTCAGCATATCAGCTGGACCTATTTCCTGAATGCAGAGTGACTCTTCTGTTATTTAAAGATGTAAAAATGCTGGA
GACTTGAGAAAGAAGGCCATGGAAGGCACCACTGATGGTGCATTGATAAATCCTTCAGTGATTGTTGATCCTTTTTAGGT
ACTTGTGGCAGCAAATAAAGCAGTTCACCTCTACTAACTGGGAAAAATGAAGACGAGAACTCTGTTTACTGAAATTATTT
TCAACCTTTCCCAAACGACAATATTTCAGAGGCTTTGAAAAAATTTGGTATCTCAGCAGATAATACTTCAATTTTTATTG
TTTATGTTGAAGAGGGAGAAAAACAAGTAAATCAAAAATACCTAATATCTCAAGTAGAGGGTCACCAGATTTCTCTGAAA
AATCTTCCTGAAATAACTAATATTTCTGAAGTCAAAAAGATTATAAGTGTCTTCACAAGAAGAAAAAATTGGGACATTAT
TGGGTGGTTATCATTAGTAGAATGTCAACAAAAGATGTTTTA

Alignment

ORF - retro_itri_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MQLTYQLDLFPECTVTLLLFKDVK-NAGDLRKKAMEGTIDGALINPSVIVDPFQILVAANKAVHLYKLGK
          MQ..YQLDLFPEC.VTLLLFKDVK.NAGDLRKKAMEGT.DGALINPSVIVDPF..LVAANKAVHLY.LGK
Retrocopy MQSAYQLDLFPECRVTLLLFKDVK<NAGDLRKKAMEGTTDGALINPSVIVDPF*VLVAANKAVHLY*LGK

Parental  MKTRTLSTEIIFNLS-PNNNISEALKKFGISADNTSILIVYVEEGEKQVNQKYLISQVEGDQISLKNLPE
          MKTRTL.TEIIFNLS.PN.NISEALKKFGISADNTSI.IVYVEEGEKQVNQKYLISQVEG.QISLKNLPE
Retrocopy MKTRTLFTEIIFNLS<PNDNISEALKKFGISADNTSIFIVYVEEGEKQVNQKYLISQVEGHQISLKNLPE

Parental  ITNISEVKKI-YK-VSSQEEKIGTLLGG-IISRMSTKDVL
          ITNISEVKKI.YK.VSSQEEKIGTLLGG.IISRMSTKDVL
Retrocopy ITNISEVKKI<YK<VSSQEEKIGTLLGG>IISRMSTKDVL

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_1613 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1613 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012021	1 retrocopy	retro_chof_35,
Callithrix jacchus	ENSCJAG00000004162	3 retrocopies	retro_cjac_1999, retro_cjac_2867, retro_cjac_3065,
Homo sapiens	ENSG00000144034	1 retrocopy	retro_hsap_552,
Gorilla gorilla	ENSGGOG00000009062	1 retrocopy	retro_ggor_501,
Macaca mulatta	ENSMMUG00000030805	1 retrocopy	retro_mmul_1571,
Monodelphis domestica	ENSMODG00000016950	2 retrocopies	retro_mdom_1264, retro_mdom_465,
Nomascus leucogenys	ENSNLEG00000000300	2 retrocopies	retro_nleu_2021, retro_nleu_957,
Oryctolagus cuniculus	ENSOCUG00000016251	2 retrocopies	retro_ocun_519, retro_ocun_769,
Otolemur garnettii	ENSOGAG00000032893	2 retrocopies	retro_ogar_523, retro_ogar_849,
Pongo abelii	ENSPPYG00000012292	1 retrocopy	retro_pabe_509,
Pteropus vampyrus	ENSPVAG00000012419	1 retrocopy	retro_pvam_75,
Ictidomys tridecemlineatus	ENSSTOG00000016406	4 retrocopies	retro_itri_1613 , retro_itri_453, retro_itri_918, retro_itri_919,
Tupaia belangeri	ENSTBEG00000014584	2 retrocopies	retro_tbel_33, retro_tbel_3630,
Vicugna pacos	ENSVPAG00000007934	2 retrocopies	retro_vpac_149, retro_vpac_192,