RetrogeneDB ID: retro_itri_1004

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:2300170..2300789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCCIP
• Ensembl ID: ENSSTOG00000011828
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:HGNC Symbol;Acc:978]

Sequence

>retro_itri_1004
GTTGACCAGGAGGTGAATGTTGAATTTGAAGCTTATTCCATCACAGATAATGATTATGACTGAATTAAGAAATTACTGCA
GCAGCTTTTCCTAAAGGCTCCTGTGAACGCTGCAGAACTAACAGATCTCTTAATTCAACAGAACCATATTGGAAGTGTGA
TTAAGCAAACAAACGTTTCAGAAGACAGCAATGATGATGATGTGGATGAAGATGAAATTTTTGGTTTCATAAGCCTTTTA
AATTTAACTTGAAAGAAAGGGTACCCAGTGTTCTGAACAAATTAAAGAGTTGGTTCTAAGCTTCTGTGAGAAGAACTGTG
AAAAGAGTATGGTCGAACAGCTGGACAAGCTTTTAAATGATATCACCAAGCCTGTGGGCTTTCTCCTAAGTGAAAGATTC
ACTAATGTCCCTCCTCAGATTGCTCTGCCCATGCACTAGCAGCTTCAGAAAGAACTAGCAGAGACGCACAAAACTAATAA
GCCATGTGAGAAGTGCTCCTTCTACCTTCTGATTAGTAAGACATTTGTGGAAGCAGGAAAATCCAATTCTAAAAAGAGGT
GGAGCAACCAGAAGGATGAATTAATGTTTATAAATGCAGAGGAAGAGTGTTTCTATGAG

Alignment

ORF - retro_itri_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 77.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDEEVNIEFEAYSISDNDYDGIKKLLQQLFLKAPVNTAELTDLLIQQNHIGSVIKQTNVSEDSDDDDADE
          .D.EVN.EFEAYSI.DNDYD.IKKLLQQLFLKAPVN.AELTDLLIQQNHIGSVIKQTNVSEDS.DDD.DE
Retrocopy VDQEVNVEFEAYSITDNDYD*IKKLLQQLFLKAPVNAAELTDLLIQQNHIGSVIKQTNVSEDSNDDDVDE

Parental  DEIFGFISLLNLT-ERKGTQCAEQIKELVLSFCEKNCEKSVVEQLDKLLNDTTKPVGFLLSERFINVPPQ
          DEIFGFISLLNLT.ERKGTQC.EQIKELVLSFCEKNCEKS.VEQLDKLLND.TKPVGFLLSERF.NVPPQ
Retrocopy DEIFGFISLLNLT>ERKGTQCSEQIKELVLSFCEKNCEKSMVEQLDKLLNDITKPVGFLLSERFTNVPPQ

Parental  IALPMHQQLQKELVESHKTNKPCGKCSFYLLISKTFVEAGKSNSKKKWSNQKDELMFVNAEEEFFYE
          IALPMH.QLQKEL.E.HKTNKPC.KCSFYLLISKTFVEAGKSNSKK.WSNQKDELMF.NAEEE.FYE
Retrocopy IALPMH*QLQKELAETHKTNKPCEKCSFYLLISKTFVEAGKSNSKKRWSNQKDELMFINAEEECFYE

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_1004 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1004 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004 , retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260, retro_tbel_2963, retro_tbel_3044,