RetrogeneDB ID: retro_itri_1682

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393632.1:1172772..1173309(+)
• Located in intron of: ENSSTOG00000014903

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSSTOG00000006223
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_itri_1682
ATGGCCTCCAATAAGACCACATTGTAAAAAATGGGAAAGAAACAGAATGGAAAGACTAAAAAAGTTGAAGAGGCAGAGCC
TGAAGAATTTGTGGCAGAAAAAGTCCTAGACTGACATGTAGTAAATGGAAAGGTGGAATACTTTCTGAAGTGGAAGGGAT
TTACAGGTGCTGACAATACTTGGGAACCTGAAGAAAATTTAGATTGTCCAGAGTGAATCGAAGCATTTCTTAATTCTCAA
AAAGCTGGTAAATAAAAAGATGGTACCAAAAGAAAATCTTTATCTGACAGTGAATCTGATGATAGCAAGTTAAAGAAGAA
AAGAGATGCTGCTGACAAACCAAGAGGCTTTGCCAGAGGTCTTGATCCTGAACGAATAATTGGTGCCACAGACAGCAGTG
GAGAATTGATGTTTCTTATGAAATGGAAAGATTCAGATGAGGCAGACTTGGTGCTGGCAAAAGAAGCAAATATGAAGTGT
CCTCAAATTGTAATTGCTTTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAG

Alignment

ORF - retro_itri_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.97 %
• Parental protein coverage: 97.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCP
          MASNKTTL.KMGKKQNGK.KKVEEAEPEEFV.EKVLD..VVNGKVEYFLKWKGFT.ADNTWEPEENLDCP
Retrocopy MASNKTTL*KMGKKQNGKTKKVEEAEPEEFVAEKVLD*HVVNGKVEYFLKWKGFTGADNTWEPEENLDCP

Parental  ELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLM
          E.IEAFLNSQKAGK.KDGTKRKSLSDSESDDSK.KKKRDAADKPRGFARGLDPERIIGATDSSGELMFLM
Retrocopy E*IEAFLNSQKAGK*KDGTKRKSLSDSESDDSKLKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLM

Parental  KWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPE
          KWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPE
Retrocopy KWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPE

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_1682 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1682 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 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005969	1 retrocopy	retro_amel_1184,
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Gorilla gorilla	ENSGGOG00000025853	6 retrocopies	retro_ggor_1928, retro_ggor_2281, retro_ggor_2466, retro_ggor_2467, retro_ggor_635, retro_ggor_845,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,
Ictidomys tridecemlineatus	ENSSTOG00000006223	4 retrocopies	retro_itri_1093, retro_itri_1682 , retro_itri_1764, retro_itri_912,
Ictidomys tridecemlineatus	ENSSTOG00000023986	3 retrocopies	retro_itri_1282, retro_itri_1599, retro_itri_1867,