RetrogeneDB ID: retro_itri_152

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:14211081..14211603(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028574
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSSTOG00000002775
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_itri_152
ATGGCTCCAATGAATCGCCCAGCTCCTGTGGAAGTCACATACAGGAACATGAGATTTCTTATTACACACAACCCAACCAG
TGCAACCTTAAACAGATTTATAGAGGAACTTAAGAAATACGGAGTTACAACAATAGTGAGAGTGTGTGAAGCAACTTATG
ACACTGCTCTTATGGAGAAAGAAGGAATCCAGGTTCTAGATTGGCCTTTTGATGATGGTTCCTCACCATCCAACCAGATT
GTTGATGACTGGTTAAGTCTTGTAAACATTAAATTTCGTGAAGAACCTGGTTGTTGTATTGCCGTTCACTGTGTTGCAGG
TCTTGGGCGAACTCCAGTGCTTGTCGCCTTAGCATTAATTGAAAGTGGAATGAAAAATGAAGATGCAGTACAGTTTATAA
GACAAAAGCGGCGCGGAGCTTTTAACAGCAAGCAACTTTTATATTTGGAGAAATATCGTTCTAAAATGCGGCTGCGCTTC
AAAGACTCCAATGGTCACAGAAACAACTGTTGCGTTCAATAA

Alignment

ORF - retro_itri_152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIYVLDWPFDDG
          MNRPAPVE..Y.NMRFLITHNPT.ATLN.F.EELKKYGVTT.VRVC.ATYD.A..EKEGI.VLDWPFDDG
Retrocopy MNRPAPVEVTYRNMRFLITHNPTSATLNRFIEELKKYGVTTIVRVCEATYDTALMEKEGIQVLDWPFDDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
          ..P.NQIVDDWL.L...KFREEPGCC.AVHCVAGLGR.PVLVALALIE.GMK.EDAVQFIRQKRRGAFNS
Retrocopy SSPSNQIVDDWLSLVNIKFREEPGCCIAVHCVAGLGRTPVLVALALIESGMKNEDAVQFIRQKRRGAFNS

Parental  KQLLYLEKYRPKMRLRFRDTNGH---CCIQ
          KQLLYLEKYR.KMRLRF.D.NGH...CC.Q
Retrocopy KQLLYLEKYRSKMRLRFKDSNGHRNNCCVQ

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_152 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_152 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
Callithrix jacchus	ENSCJAG00000006539	2 retrocopies	retro_cjac_3257, retro_cjac_566,
Homo sapiens	ENSG00000184007	4 retrocopies	retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Mus musculus	ENSMUSG00000028788	2 retrocopies	retro_mmus_1894, retro_mmus_2432,
Nomascus leucogenys	ENSNLEG00000002137	3 retrocopies	retro_nleu_2880, retro_nleu_2956, retro_nleu_3015,
Oryctolagus cuniculus	ENSOCUG00000002060	1 retrocopy	retro_ocun_1673,
Otolemur garnettii	ENSOGAG00000029603	1 retrocopy	retro_ogar_3341,
Pongo abelii	ENSPPYG00000001606	3 retrocopies	retro_pabe_1507, retro_pabe_808, retro_pabe_890,
Rattus norvegicus	ENSRNOG00000050044	1 retrocopy	retro_rnor_305,
Sus scrofa	ENSSSCG00000003605	1 retrocopy	retro_sscr_1186,
Ictidomys tridecemlineatus	ENSSTOG00000002775	2 retrocopies	retro_itri_1165, retro_itri_152 ,
Tupaia belangeri	ENSTBEG00000006790	1 retrocopy	retro_tbel_4601,
Tursiops truncatus	ENSTTRG00000016571	2 retrocopies	retro_ttru_1396, retro_ttru_1402,