RetrogeneDB ID: retro_itri_1513

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393519.1:1621664..1622101(-)
• Located in intron of: ENSSTOG00000015861

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_1513
GAAGATGAAATCCAGGATGAGGATGAAGATGATGGGGACAGTGACAAAGAAGAGAATGAAAGTGACCAGACCACTGGCAA
GGAAGTAAACACTGAATCTGAAGCTCGTTCCATCTCAGATAACGATGGGGATGAAATGAAGAAATCACTGCGGCTTTTCC
AAAGGCTTCACCCAAAGCCTCCTATGAACAGTGCAGAACTAACAGACCTCTTAATTGGCCAGAACCGCAGTGGGAATGTG
ATTAAGAATGTTTCAGACACAGAAATGACGATGCGGATGAAGATGAGATTTTTTTGGTTTCATAAGCCTTTTAAATTTCA
CTGGAAGAAAGGATGTCCAGTGTGCTGAACAAATTAAAGAGTTGATTTTTAAGCTTCTGTGAGAAGAACCGTGAATAGAT
CATGGTGAAACAGCCGGAGAAGCTTTTAAAACTGACA

Alignment

ORF - retro_itri_1513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.94 %
• Parental protein coverage: 54.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDEVEDEDEDDEESDEEEDEDDEVLDEEVNIEFEAYSISDNDYDGIKK---LLQQLFLKAPVNTAELTDL
          EDE..DEDEDD..SD.EE.E.D.....EVN.E.EA.SISDND.D..KK...L.Q.L..K.P.N.AELTDL
Retrocopy EDEIQDEDEDDGDSDKEENESDQTTGKEVNTESEARSISDNDGDEMKKSLRLFQRLHPKPPMNSAELTDL

Parental  LIQQNHIGSVIKQTNVSEDS-DDDDADED-EIFGFISLLNLTERKGTQCAEQIKELV-LSFCEKNCEKSV
          LI.QN..G.VIK..NVS.....DD........FGFISLLN.T.RK..QCAEQIKEL..LSFCEKN.E...
Retrocopy LIGQNRSGNVIK--NVSDTE<NDDADEDE<DFFGFISLLNFTGRKDVQCAEQIKELI>LSFCEKNRE*IM

Parental  VEQLDKLLNDT
          V.Q..KLL..T
Retrocopy VKQPEKLLKLT

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_1513 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1513 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,