RetrogeneDB ID: retro_itri_23

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393457.1:4039175..4039424(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025727
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NDUFA4L2
• Ensembl ID: ENSSTOG00000020476
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 [Source:HGNC Symbol;Acc:29836]

Sequence

>retro_itri_23
ATGCTCCGCCAGATCCTTGGTCAGGCCAAGAAGCATCCAAGCTTGATTCCCCTCTTCGTATTTATTGGAGCAGGAGGTAC
TGGAGCAGCACTGTATGTGATGCGTCTAGCATTGTTCAATCCAGATGTCAGTTGGGATAGGAAGAATAACCCAGAACCCT
GGAACAAACTGGGTCCTAATGATCAATACAAGTTCTACTCAGTGAATGTGGATTACAGCAAACTGAAGAAAGAAGGCCCA
GACTTCTAA

Alignment

ORF - retro_itri_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.0 %
• Parental protein coverage: 86.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIKRHPGLIPMIGFIGLGMGSAALYLLRLALRSPDVCWDRKNNPEPWNRLSPNDQYKFLAVSTDYKKLKK
          Q.K.HP.LIP...FIG.G...AALY..RLAL..PDV.WDRKNNPEPWN.L.PNDQYKF..V..DY.KLKK
Retrocopy QAKKHPSLIPLFVFIGAGGTGAALYVMRLALFNPDVSWDRKNNPEPWNKLGPNDQYKFYSVNVDYSKLKK

Parental  DRPDF
          ..PDF
Retrocopy EGPDF

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_23 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_23 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 7 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000004466	1 retrocopy	retro_etel_52,
Homo sapiens	ENSG00000185633	2 retrocopies	retro_hsap_4698, retro_hsap_4857,
Loxodonta africana	ENSLAFG00000021950	1 retrocopy	retro_lafr_21,
Macropus eugenii	ENSMEUG00000014358	3 retrocopies	retro_meug_1159, retro_meug_1559, retro_meug_467,
Nomascus leucogenys	ENSNLEG00000017371	10 retrocopies	retro_nleu_1015, retro_nleu_1048, retro_nleu_1851, retro_nleu_1917, retro_nleu_2588, retro_nleu_2952, retro_nleu_363, retro_nleu_732, retro_nleu_862, retro_nleu_956,
Ictidomys tridecemlineatus	ENSSTOG00000020476	1 retrocopy	retro_itri_23 ,
Tupaia belangeri	ENSTBEG00000015731	5 retrocopies	retro_tbel_3586, retro_tbel_4134, retro_tbel_4193, retro_tbel_822, retro_tbel_865,