RetrogeneDB ID: retro_itri_1454

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393493.1:588001..588425(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023848
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSSTOG00000005153
• Aliases: None
• Description: Nedd4 family interacting protein 1 [Source:HGNC Symbol;Acc:17592]

Sequence

>retro_itri_1454
AGGTTGAAAGCTGAAGCTACCATCCCTTTAGTTTCTGGAAGAGATGAAGATTTTATGGGCCGGGATGATTTTGATGATGC
TGAACAGCTGAGGATAGGAAGTGATGGGACTTTCATGTTAACTTTTTTCATGGCATTCGTCTTCAACTGGATTGAGTTTT
TCCTATCTTTTTGCCTGACCACCTCAGCTGCAGGAAGGTATGAGGCCTTCTCAGGATTTGGTCTCTCTCCAATTAAGTGG
ATCCTGATTGTCAAGTTTTCCACCTATTTCCCTGGATACTTTGATGGTTCAGTACTGGTTCTGGTGGGTGTTCCTGGTTT
TAGGCTCTCTCCTGTTTCTCAGAGGATTTGTCAATTATGCAAAAGTCCGGAAGATGCCAGAAACTTTCTCAAATCTCCCC
AGGACCAGAGTTCTCTTTACTTAT

Alignment

ORF - retro_itri_1454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 63.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTKAEATIPLVPGRDEDFVGRDDFDDADQLRIGNDGIFMLTFFMAFLFNWIGFFLSFCLTTSAAGRYGAI
          R.KAEATIPLV.GRDEDF.GRDDFDDA.QLRIG.DG.FMLTFFMAF.FNWI.FFLSFCLTTSAAGRY.A.
Retrocopy RLKAEATIPLVSGRDEDFMGRDDFDDAEQLRIGSDGTFMLTFFMAFVFNWIEFFLSFCLTTSAAGRYEAF

Parental  SGFGLSLIKWILIVRFSTYFPGYFDG-QYWLWWVFLVLGFLLFLRGFINYAKVRKMPETFSNLPRTRVLF
          SGFGLS.IKWILIV.FSTYFPGYFDG.QYW.WWVFLVLG.LLFLRGF.NYAKVRKMPETFSNLPRTRVLF
Retrocopy SGFGLSPIKWILIVKFSTYFPGYFDG>QYWFWWVFLVLGSLLFLRGFVNYAKVRKMPETFSNLPRTRVLF

Parental  IY
          .Y
Retrocopy TY

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_1454 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1454 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454 ,