RetrogeneDB ID: retro_itri_1469

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393499.1:1504359..1505518(-)
• Located in intron of: ENSSTOG00000026038

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSSTOG00000006596
• Aliases: None
• Description: pentatricopeptide repeat domain 2 [Source:HGNC Symbol;Acc:25734]

Sequence

>retro_itri_1469
GCCCAGGACAATATGGCTGCATTTCGGTCCTTGGAAGGAGCTTTGCAGCAAACGACATGGACTTCTTTTTATCCCAGGGT
GGAAGGAACAGGCTCCAACTGCTGCCGGTGCCCTCTCAGAGCTAAACGATATCTACTTACACATAATATCATGAAATTAA
AAGAATTTCAACATAAGAAATTGGCTGTTGCATATAATCTTCCTGGCACCAAAGAAACCTATTTTAGAAACTTGGAAGAG
AAATTGACCCAGAACAAACTCATCTTAAAGGACGAATTGAGAACTTTGCTTCATTTGAGTCAGACTCAGGATGATGTGGA
GCTGGCTAAAAATGTCATGTACAGGTACCATACAGAGAACAGAAATGTCACTTTGGCGGAGTAGAAGTTTGGACCAGTTT
TCATGAGGCTGTGTTATGAGTTGGATCTTGAGGAGTCTGCAATGGAGCTCATCAAAGACCAGCATTTACACGGTTTCTTC
TCAGACTCCACATCATTCAGTATTTTGATGGATATGTTATTTATCAAAGGCAAATATAAAAATGCCTTGGAAGTGTTGAT
AGAGATGAAAAACAAAGATGTGAAGTTCACCAAAGATACCTATGTCCTTGCTTTTGCAATTTTGCTACACACTGAATAGC
CCATAGTCTTTTAAAATCTGTACTACATTAAGAGAAGAAGCTTTAATCAAGGAGACGTTCTGTCCAGGAGAGCCTGCTGC
TTTGCAGTGGTGTTAGCTCTGAACCAGAACCAGGTAGCAAAAGCTGCATCCATTTTTTTCTCAAATCATGAATCCAGAGA
GCATAACTTGCACAAATTTAAATATTATAATCCATATCCAGTCAAATATGTTGGAAACCCTGATAGATATACTAACGAAT
ACTGCAGAAGGAAATTTATCAAGATTTGTGAAAAAACATGAGTTCTCAGAGGAAGTGTTGGTCAAGGTTAGGGAAAAAGT
GAAGGATGCACCCAACCTTCTGGCCAAATTTGACGAGATCTATGGGAAACTGCACATAAATGGCCAGGTCACCACTTACA
CATTGGATACTCTGCTCTGCCATACCCTCAGGGACAGGAAGTCCTATACATTGCTATTAAACAAGAGGACAATCAGCCGT
TGGAGCTTCCAGCCCCTCAGCCAGTCCCTGTTGGCTGAG

Alignment

ORF - retro_itri_1469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARDNMAAFRSLERALQQTTRTSFYPGVEAAGSNCCRCPLGAKRYLLTDNIMKLKEFQHKKLAIAYNLPDT
          A.DNMAAFRSLE.ALQQTT.TSFYP.VE..GSNCCRCPL.AKRYLLT.NIMKLKEFQHKKLA.AYNLP.T
Retrocopy AQDNMAAFRSLEGALQQTTWTSFYPRVEGTGSNCCRCPLRAKRYLLTHNIMKLKEFQHKKLAVAYNLPGT

Parental  KETYFRNLEEKLTQNKLILKDELRTLLHLCQTRDDVELAKNVMYRYHTENRNVTLGEYKFGPVFMRLCYE
          KETYFRNLEEKLTQNKLILKDELRTLLHL.QT.DDVELAKNVMYRYHTENRNVTL.E.KFGPVFMRLCYE
Retrocopy KETYFRNLEEKLTQNKLILKDELRTLLHLSQTQDDVELAKNVMYRYHTENRNVTLAE*KFGPVFMRLCYE

Parental  LDLEESAVELIKDQHLHGFFSDSTSFNILMDMLFIKGKYKNALEVLIEMKNQDVKFTKDTYVLAFAI-CY
          LDLEESA.ELIKDQHLHGFFSDSTSF.ILMDMLFIKGKYKNALEVLIEMKN.DVKFTKDTYVLAFAI.CY
Retrocopy LDLEESAMELIKDQHLHGFFSDSTSFSILMDMLFIKGKYKNALEVLIEMKNKDVKFTKDTYVLAFAI>CY

Parental  RLNSPESFKICTTLREEALIK-GDVLSRRASCFAVALALNQNQVAKAASI-FSQIMNPENITCTNLNIII
          .LNSP.SFKICTTLREEALIK.GDVLSRRA.CFAV.LALNQNQVAKAASI.FSQIMNPE.ITCTNLNIII
Retrocopy TLNSP*SFKICTTLREEALIK<GDVLSRRACCFAVVLALNQNQVAKAASI>FSQIMNPESITCTNLNIII

Parental  HIQSNMVETLIDILTNAAEGNLSIFVKKRVFSEEVLVKVREKVKDDAPNLLAKFDEIYGKLHINGQITTY
          HIQSNM.ETLIDILTN.AEGNLS.FVKK..FSEEVLVKVREKVK.DAPNLLAKFDEIYGKLHINGQ.TTY
Retrocopy HIQSNMLETLIDILTNTAEGNLSRFVKKHEFSEEVLVKVREKVK-DAPNLLAKFDEIYGKLHINGQVTTY

Parental  SLDTLLCRTPRDKKSHTLLLNKRTISRRTFQPLSQSLLAE
          .LDTLLC.T.RD.KS.TLLLNKRTISR..FQPLSQSLLAE
Retrocopy TLDTLLCHTLRDRKSYTLLLNKRTISRWSFQPLSQSLLAE

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_1469 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1469 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469 ,