RetrogeneDB ID: retro_itri_408

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:16707950..16708911(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZSCAN4
• Ensembl ID: ENSSTOG00000023779
• Aliases: None
• Description: zinc finger and SCAN domain containing 4 [Source:HGNC Symbol;Acc:23709]

Sequence

>retro_itri_408
ATGACATTACATCTCAAAAATTCATTTCAATGTGAAACACCCCAATATGATGTTGATTAGAAAATATAAAATTTAGACCA
ATCCAAGGATCTGCTGTTCAGAAGGGAGAGGAGATTTCTTGAGTTCTCATGCTCTCAGCTCAACTCATTTTAATAAGCAA
TAACTCATGTGCAAGGCAAAAATTGCAAAGATTCCATGAGATTTTTCATTCATGGGTGCAACCAGAAAAGCATAGTAAGG
ATTAAATTATTTCTCAACTGGTCCTGGAGCAGTTTATGATTAATGGAAACTGCAGGGACAAATTCACTTTGAAAGGGAAA
TGGGAATCAATGGCAGAATCTGGAGAAATTAATGGAAGAACTGATCTATGATTGTGTGAAGCCACTTGTCATAGTCCATG
TTCCCATGCAGGGACAGGAAACCCTTTTGTTCTGAGACTATGCCCTTAAGAGAAGTCCTTATTCATCTCAAAAACCCGTT
GTCAGCAGAACACAACAGCAGAGAAATACTGATACCCTTTGAGAAATCTCCAGATACTTACTTGGAAAAAAGACAAGAAG
ATAAAGAAGATGGATATAACAATTCCTGGAAAAATGCTCAAGTAAATGACACTGTTAATAGTTAACGGACTCACATATTT
TCCCTGTTCATTTTCCAGGAAGAGGACTATCCTAGGTCTAAAGAGAAAGATGTTTGTTGTGAGATACTCACACAACTCCA
GAAGAGCAAGGGTAGGTACCTCTAATTCCCAGAAAGGGTCCCTGAAATGACCTTATCAAAACATCACTGTGGAGGTGCAA
CCTATACTTCTCTCTAAGCCAGACAGTCCTCTAAGCCTGTCCCTACCTACCTGAGCAAGGAGGGAACTTCCACATGTGAG
GGACATCAAGAGAAATTCCATAAAGCCCCAAAATCATACAAGTGAGAGAAATGTCCCAAGGTTTTTAGGTCATTTGTTCA
T

Alignment

ORF - retro_itri_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.09 %
• Parental protein coverage: 98.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MPSNLTNSCQCKTSQNDFE-LGNTEFRRTQGSAVQNGEIFS-EFSSSQLNS-LPDNGNSNARKELQRLHG
          M...L.NS.QC.T.Q.D...L.N..FR..QGSAVQ.GE..S.EFS.SQLNS......NS.AR..LQR.H.
Retrocopy MTLHLKNSFQCETPQYDVD<LENIKFRPIQGSAVQKGEEIS>EFSCSQLNS<ILISNNSCARQKLQRFHE

Parental  IFHSWLQPEKHSKDEIISRLVLEQFMINGNCRDRSILKEKWES-SGR-NLEKLMEDLTDDCMEPPVLVRV
          IFHSW.QPEKHSKD.IIS.LVLEQFMINGNCRD...LK.KWES..GR.NLEKLME.L..DC..P.V.V.V
Retrocopy IFHSWVQPEKHSKD*IISQLVLEQFMINGNCRDKFTLKGKWES<NGR<NLEKLMEELIYDCVKPLVIVHV

Parental  HMQGQEALF-SENMPLKEVIVHLKKQLSAENTTGENKGMSLQAPQDTPLETRQGNEDKENACNNFWKNTQ
          .MQGQE.L..SE.MPL.EV..HLK..LSAE....E..........DT.LE.RQ..EDKE...NN.WKN.Q
Retrocopy PMQGQETLL>SETMPLREVLIHLKNPLSAEHNSREIL-IPFEKSPDTYLEKRQ--EDKEDGYNNSWKNAQ

Parental  VDDSITCQGTQTPSLLIIQEDHCLRLEDGGASCE-NPHNSRRG--VTSHSEKGPLEGPSYQNIPVGEQPE
          V.D......T...SL.I.QE....R.......CE...HNSRR....TS.S.KG.L..P.YQNI.V..QP.
Retrocopy VNDTVNS*RTHIFSLFIFQEEDYPRSKEKDVCCE>YSHNSRRARVGTSNSQKGSLK*P-YQNITVEVQPI

Parental  FLPTSD-QSSSEFVPAHQSNKGDSTCGGHHEKYRGAQKSYKCKECPKIFRYLCH
          .L...D.QSS...VP...S..G.STC.GH.EK...A.KSYK...CPK.FR...H
Retrocopy LLSKPD<QSSKP-VPTYLSKEGTSTCEGHQEKFHKAPKSYK*EKCPKVFRSFVH

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_408 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_408 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470, retro_cpor_285,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408 ,