RetrogeneDB ID: retro_itri_1435

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393486.1:2859804..2860494(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025010
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAA10
• Ensembl ID: ENSSTOG00000010237
• Aliases: None
• Description: N(alpha)-acetyltransferase 10, NatA catalytic subunit [Source:HGNC Symbol;Acc:18704]

Sequence

>retro_itri_1435
ATGAACATCCGCAATGCTCGGCCAGACGACCTGATGAACATGCAACACTGCAACCTCCTCTGCCTTCCCGAGAACTACCA
GATGAAATACTATTTCTACCATGGCCTTTCCTGGCCTCAGCTCTCCTACATCGCTGAGGACGAGGACGGGAAGATTGTGG
GCTATGTCCTGGCCAAAATGGAAGAGGACCCTGATGATGTCCCCCATGGGCATATCACCTCACTGGCTGTGAAGCGCTCA
CACCGGCGCCTCGGCCTGGCTCAGAAGCTGATGGACCAGGCCTCGCGGGCCATGATAGAGAACTTTAGTGCCAAGTATGT
GTCCCTGCACGTCAGGAAGAGTAACCGGGCGGCCTTGCACCTCTATTCTAACACTCTCAACTTTCAGGTCAGTGAGGTGG
AACCCAAATACTATGCAGATGGGGAAGATGCTTATGCTATGAAGCGGGATCTCTCACAAATGGCAGATGAGCTAAGAAGG
CAGCCGGAGCTGAAGGAGAAGGGCGGGTATGTGGTGCTGGGCTCCAGGGAGAACCAGGAGAGCCAGAGCAGCACACTTCC
TGGTTCTAAAACGACCTGTCAGCAGGAGAACCCGGCTGTCCCTGATAGTGGGAGTGACAGCAAGGAACCTAGCGAATCCA
CGGGGAGCACCGATGTCCAGGACAGCTCAGAAGACTTGGATTCCGCCTCC

Alignment

ORF - retro_itri_1435 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNIRNARPEDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDENGKIVGYVLAKMEEDPDDVPHG
          MNIRNARP.DLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDE.GKIVGYVLAKMEEDPDDVPHG
Retrocopy MNIRNARPDDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDEDGKIVGYVLAKMEEDPDDVPHG

Parental  HITSLAVKRSHRRLGLAQKLMDQASRAMIENFNAKYVSLHVRKSNRAALHLYSNTLNFQISEVEPKYYAD
          HITSLAVKRSHRRLGLAQKLMDQASRAMIENF.AKYVSLHVRKSNRAALHLYSNTLNFQ.SEVEPKYYAD
Retrocopy HITSLAVKRSHRRLGLAQKLMDQASRAMIENFSAKYVSLHVRKSNRAALHLYSNTLNFQVSEVEPKYYAD

Parental  GEDAYAMKRDLTQMADELRRHLELKEKGRHVVLGAIENKVESKGNSLPSSGEVCREEKGLAAEDSGGDSK
          GEDAYAMKRDL.QMADELRR..ELKEKG..VVLG..EN..ES....LP.S...C..E...A..DSG.DSK
Retrocopy GEDAYAMKRDLSQMADELRRQPELKEKGGYVVLGSRENQ-ESQSSTLPGSKTTCQQENP-AVPDSGSDSK

Parental  DLSEVSETTESTDVKDSSEASDSAS
          ...E.SE.T.STDV.DSSE..DSAS
Retrocopy ---EPSESTGSTDVQDSSEDLDSAS

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_1435 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1435 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 22 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018457	1 retrocopy	retro_amel_162,
Bos taurus	ENSBTAG00000047702	1 retrocopy	retro_btau_177,
Canis familiaris	ENSCAFG00000019415	1 retrocopy	retro_cfam_167,
Callithrix jacchus	ENSCJAG00000014506	1 retrocopy	retro_cjac_132,
Equus caballus	ENSECAG00000015203	1 retrocopy	retro_ecab_717,
Felis catus	ENSFCAG00000028705	1 retrocopy	retro_fcat_51,
Homo sapiens	ENSG00000102030	1 retrocopy	retro_hsap_13,
Gorilla gorilla	ENSGGOG00000009788	1 retrocopy	retro_ggor_196,
Macropus eugenii	ENSMEUG00000006054	2 retrocopies	retro_meug_1787, retro_meug_554,
Myotis lucifugus	ENSMLUG00000014267	1 retrocopy	retro_mluc_152,
Macaca mulatta	ENSMMUG00000000322	1 retrocopy	retro_mmul_21,
Mustela putorius furo	ENSMPUG00000008989	1 retrocopy	retro_mputfur_1424,
Mus musculus	ENSMUSG00000031388	1 retrocopy	retro_mmus_1416,
Nomascus leucogenys	ENSNLEG00000013724	1 retrocopy	retro_nleu_57,
Otolemur garnettii	ENSOGAG00000013263	1 retrocopy	retro_ogar_260,
Pongo abelii	ENSPPYG00000020861	1 retrocopy	retro_pabe_2530,
Pan troglodytes	ENSPTRG00000022419	1 retrocopy	retro_ptro_23,
Pteropus vampyrus	ENSPVAG00000000463	1 retrocopy	retro_pvam_1225,
Sarcophilus harrisii	ENSSHAG00000005952	1 retrocopy	retro_shar_362,
Sus scrofa	ENSSSCG00000012791	1 retrocopy	retro_sscr_987,
Ictidomys tridecemlineatus	ENSSTOG00000010237	1 retrocopy	retro_itri_1435 ,
Tursiops truncatus	ENSTTRG00000007455	1 retrocopy	retro_ttru_198,