RetrogeneDB ID: retro_itri_1485

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393506.1:930858..931900(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF131
• Ensembl ID: ENSSTOG00000015383
• Aliases: None
• Description: zinc finger protein 131 [Source:HGNC Symbol;Acc:12915]

Sequence

>retro_itri_1485
CACAAACAGAAACACATGAAATCGTACTCTACTGAGAATTTCAAGTGCCAAATATGCAATAAAAGTTACCTTCCATATAG
CACTTGGAAATAGTACCTAAATTGTTACCACCTTGAAGAAGGTGGAGTCAGTAAGAAGCAAAGAACTGGGGGAAAAATAA
TATGTCAGTACTATGAGAAACAGTTTGACCACTTTGGATATTTTAAAGAGCATATTTGAAAACATACAGGTGAAAAACCT
TTGGGTTTCCAAATTGTCATGAATTATATACTAGAAATAGTAACCTCAAATGTCATCTCACTGCATGCCAAACTGGAGTG
GGAGCAAAAATGGGAAGGAACAAGCTGTATGAATGCCAGGTGTATAACAGTGTGCTTAAATGTTAGGACCAGTTCAAAAG
TCACTTGGTGATACACGCTGCAGATAAACCCAATCATTGTACTCTATGTGACTTGTGACTTATGCAAGGAAATGAATTAA
GGAGGCAAATCAGTGATACTAATAATATTTCAGAGCATCTAGTAATTACAGAAGTCCTTTCAGTAGCAACATGTGTGCAA
ACTGAACCAGTGATATCAATGACTATTATAGAACTAGTTGGGAATGTGCATTTGTTACCATTACTTCAGGTCCAGGTGGA
TTCAGCACAAGTGACTGTGGAACAAGTCCATCCTGATCTGCTTAAGGACAGCCAGTTGCATGATTCATACATGAGGGAGC
TTCCAGAGCAAGTCCAAGTCAGTTATCTAGAAGTAGGTTGAATTCAGACTGAAGAAGATACTGAAGTACAGGTAGATGAG
CTGCATGTTGAAGAGGTAAATCAGATGCCAGTGGAAGTACAATCTGAGCTTCTAGAAGAGGACTTCAATCACGTGACCTC
TGAAATCATGAGCCAAGAGGAGAGAGAGACAAATCGAAAAGATGCTGCTGAGGCTGCCAGGGAAGATCACAAAGGTGCTG
AGAGTTTAAAGACCAAACCAATGATGGATTCCAAGTTGAAAAGGCAGAGAATGATGACAGAACAGCTCTTCCAGTTTTAG
AT

Alignment

ORF - retro_itri_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.2 %
• Parental protein coverage: 57.52 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HFKEHMKSHSTESFKCEICNKRYLRESAWKQHLNCYHLEEGGVSKKQRTGKKIHICQYCEKQFDHFGHFK
          H...HMKS.STE.FKC.ICNK.YL..S.WK..LNCYHLEEGGVSKKQRTG.KI.ICQY.EKQFDHFG.FK
Retrocopy HKQKHMKSYSTENFKCQICNKSYLPYSTWK*YLNCYHLEEGGVSKKQRTGGKI-ICQYYEKQFDHFGYFK

Parental  EHLRKHTGEKP-FECPNCHERFARNSTLKCHLTACQTGVGAKKGRKKLYECQVCNSVFNSWDQFKDHLVI
          EH..KHTGEKP.F..PNCHE...RNS.LKCHLTACQTGVGAK.GR.KLYECQV.NSV....DQFK.HLVI
Retrocopy EHI*KHTGEKP<FGFPNCHELYTRNSNLKCHLTACQTGVGAKMGRNKLYECQVYNSVLKC*DQFKSHLVI

Parental  HTGDKPNHCTLCDLWFMQGNELRRHLSDTHNISERLVTEEVLSVETRVQTEPVTSMTIIEQVGKVHVLPL
          H..DKPNHCTLCDL..MQGNELRR..SDT.NISE.LV..EVLSV.T.VQTEPV.SMTIIE.VG.VH.LPL
Retrocopy HAADKPNHCTLCDL*LMQGNELRRQISDTNNISEHLVITEVLSVATCVQTEPVISMTIIELVGNVHLLPL

Parental  LQVQVDSAQVTVEQVHPDLLQDSQVHDSHMSELPEQVQVSYLEVGRIQTEEGTEVHVEELHVERVNQMPV
          LQVQVDSAQVTVEQVHPDLL.DSQ.HDS.M.ELPEQVQVSYLEVG.IQTEE.TEV.V.ELHVE.VNQMPV
Retrocopy LQVQVDSAQVTVEQVHPDLLKDSQLHDSYMRELPEQVQVSYLEVG*IQTEEDTEVQVDELHVEEVNQMPV

Parental  EVQTELLEADLDHVTPEIMSQEEREPNQADAAEAAREDHRGAEGLKTKPAVDS-QVEKAEN-DRTAMPVL
          EVQ.ELLE.D..HVT.EIMSQEERE.N..DAAEAAREDH.GAE.LKTKP..DS.QVEKAEN.DRTA.PVL
Retrocopy EVQSELLEEDFNHVTSEIMSQEERETNRKDAAEAAREDHKGAESLKTKPMMDS<QVEKAENDDRTALPVL

Parental  D
          D
Retrocopy D

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_1485 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1485 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001280	1 retrocopy	retro_cjac_2484,
Cavia porcellus	ENSCPOG00000011858	1 retrocopy	retro_cpor_350,
Gorilla gorilla	ENSGGOG00000002252	1 retrocopy	retro_ggor_2485,
Ictidomys tridecemlineatus	ENSSTOG00000015383	1 retrocopy	retro_itri_1485 ,
Tursiops truncatus	ENSTTRG00000009644	1 retrocopy	retro_ttru_418,