RetrogeneDB ID: retro_itri_543

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:9623823..9624718(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000006504
• Aliases: None
• Description: None

Sequence

>retro_itri_543
ATCATACCATAGAGGTGTGATTCTTATGATATTTCATATCTTTAGCCCATGGATGACCTGGGCCAGATTATCTTTCTGGA
AAGGAATGGAAGAGACAGAGATTCTATCCGAAGAGCACGGGAACACAGCAATGTGGTCATCAATCTTGTTGGATGAGACT
GGGAAACCAGAAACTTTGATTTTTGAGGATATTTTCATGAAGACTCCCCCAAGCATTACCTCAAAGTTCTAAGGAAGCTG
GAGTTGAAAATTTCATCCATGTTTCCCCCTCTGAATGTGGATACTAGAAGCACTTCTAGATATCTGAGAGAGAAGGCTGT
TGGAGAGAAGGAAGTGAGAAATGCATTTCCAGAATCTACCATCATAAAACCATCAGACATCTTTGGAAGAGAGGATAGAT
TCCTCAACCATATTGTAAATATTCGTTGGGTTTGGTGGTGCACCTCTTATTTCCTTGGGCAGGAAGACTGAGAAACAACC
AATATATGTTGTGGATGTATCCAAAGGAATTATTAATACATTTAAAGACCCAGATGCCAGAGGAAAAACTTTTGCCTTTG
TTGGGCCCAGTCGGTACCTCCTCTTTGACCTGGTGCAGGACTTCTTTGCTATGGCTCACAGACCCTTCCTCTTCTATCTC
TTGCCATGCTTTGCCTATCAGTTGATAGCAAAACTCTTTAAAATAAAACCATTTGAGCCCTGGACAACAAGGGATAAAGT
GGGATGGACGCACATCAGAGACATGACATTGCCTAATCTGCCCTGCTTAGAAGACCTTGATATTCAGGTAGTTCTACTGG
AACTAAAGGCCTTTGAGGTGCTATGGCATCATTGCACTTATCGCTAGCTGTCTTCTGAAACTGAGGATATAAAATCCGCC
AAGACTGTCAGCATT

Alignment

ORF - retro_itri_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 78.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IIPYRCDPYDVMHLRPMGDLGQIIFLEWNGRDKDSIRRAVEHSNVVINLVGRDWETRNFDF-EDVFVK-I
          IIP.RCD.YD...L.PM.DLGQIIFLE.NGRD.DSIRRA.EHSNVVINLVG.DWETRNFDF.ED.F.K..
Retrocopy IIP*RCDSYDISYL*PMDDLGQIIFLERNGRDRDSIRRAREHSNVVINLVG*DWETRNFDF>EDIFMK>L

Parental  PQTIAQISKEAGVEKFIHVSH-LNANIRSSSRYLRNKAVGENEVRNAFPEATIIKPSDIFGREDRFLNHF
          PQ...Q.SKEAGVE.FIHVS..LN...RS.SRYLR.KAVGE.EVRNAFPE.TIIKPSDIFGREDRFLNH.
Retrocopy PQALPQSSKEAGVENFIHVSP>LNVDTRSTSRYLREKAVGEKEVRNAFPESTIIKPSDIFGREDRFLNHI

Parental  ANIRW-FGGVPLISLGRKTVWHDVGILDISVRNLIYGLKKPKALDKKSHIYTEPQKDFLFHPWKWCFAIA
          .NIRW.FGG.PLISLGRKT........D.S....I...K.P.A..K.......P....LF......FA.A
Retrocopy VNIRW>FGGAPLISLGRKTEKQPIYVVDVS-KGIINTFKDPDARGK-TFAFVGPSRYLLFDLVQDFFAMA

Parental  SLLNFLFPEPLLLGRWIARLFEISPFEPWTTRDKVERIHITDMTLPHLPGLEDLGIQASPLELKAIEVLR
          .........P......IA.LF.I.PFEPWTTRDKV...HI.DMTLP.LP.LEDL.IQ...LELKA.EVL.
Retrocopy HRPFLFYLLPCFAYQLIAKLFKIKPFEPWTTRDKVGWTHIRDMTLPNLPCLEDLDIQVVLLELKAFEVLW

Parental  RHRTYRWLSSEIEDVKPAKTVNV
          .H.TYR.LSSE.ED.K.AKTV..
Retrocopy HHCTYR*LSSETEDIKSAKTVSI

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_543 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_543 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
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543 ,