RetrogeneDB ID: retro_itri_170

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393557.1:1129828..1131214(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022742
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSSTOG00000002785
• Aliases: None
• Description: LSM14A, SCD6 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24489]

Sequence

>retro_itri_170
ATGAGCTGGGGCACCCCTTACCTCGGCAGCAACATTAGCCTCATCTCTAAAGCGGAGATCCGCTATGAGGGCATCCTCTA
CACCATCGACACCGAGAACTCCACTATAGCCCTCGCCAAAGTTCGATCCTTTGGTACAGAAGACAGACCAACAGATCGGC
CCGTACCACCTCGAGATGAAGTCTTTGAATATATTATCTTCCGTGGGAATGATATTAAAGATCTGACCGTTTGCGAGCCT
CCCAAACCACAATGTTCTTTGCCTCAGGACTCAGCTATCATTCAGTCTTCGCTAGGTTCGTCTCCGTTCCAGTCAGTGGG
TTCCTACGGACCTTTTGGCAGCATGCCCATGTACAGTCAGTTCAGTCTAAGTTCATTGGTCGGGCAGCAGTTTGGTGCTC
TTGGTGTTGCTGGAAGCTCCTTGCCATCCTTTGGAATGGAGACATCAAACAGTGATACCTTATCCCAAAGTAGTGCAATT
GGTTCTGCCTTTATACAGGATACAAGAACTATAAAAACACAGTCATTTCAAGGTCGTTCAAGCCCTCAGTTAGACCCTTT
GAGAGAAAGTCCAACCATGGAACAAGCAGTACAGACTGCCCCGGCCCACTTACCTGCTCCAGCACCTGTTGGGAGAAGGA
GCCCTGTATCAACCCCGCCTTTGCCATCTACCGGCCAAAAAACAATAGAGAATCAAGAGCACAAGCAAGCTGAAGTACCC
AACGTTTCAAGGTCAGAAAATGAGCAACTCAGAAATCATAGTAAGAGACAAGTAGTTCCAGGTGCTTCGTCAGCTCCAAG
AAAAGGGCGTGGGGGTCATCGATGTGGCAGGAGATTTGGTATTCAGCGATATGGTCCAATGAAATTTGAGAATGACTTTG
ACTTTGAACGTGCAAATGCACAATTTAACAAGGAGGAGATTGACAGAGAGTTTCATAATAAACTGAAATTAAAAGAAGAT
AAACTTCAGAAAAAAGAGAAGCCAGTAAATGGTGAAGGTAAAGGAGTTGATACCCAAAACAGTGAAGAAGACACTGATGA
AGAAGATCCACTTGGACCTAATTGCTATTATGACAAAAGTAAATCCTTCTTTGACAATATTTCTTATAATATTAATAGGG
AACAGAGGCCAACCTGGGCTGAAGAAAGAAGATTAAATGCTGAAACATTTGGAATTCCACTTCATCCAAACCATGGTGGT
GGGAGGTACAGAAGCAGAAGAGGTCTGAGTTTCCGTGGCAACAGAAGGCCTAGTGGTGGCAGAGGTGGCACATTTACTAC
CCCTCGAGGATTTCACTGGGGTTTTCACCGCGGATTCCGAAGAGGGCACTGGGGCAGGGAGTTTGCAGATTTTGAATACA
GGAAAAACAACAAAGTTGCTGCATAG

Alignment

ORF - retro_itri_170 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.45 %
• Parental protein coverage: 98.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLSQSSAVGSAFTQDTRSIKTQLSQGRSSPQL
          MP.YSQFS.SSLVGQQFGA.GVAGSSL.SFG.ETSNS.TLSQSSA.GSAF.QDTR.IKTQ..QGRSSPQL
Retrocopy MPMYSQFSLSSLVGQQFGALGVAGSSLPSFGMETSNSDTLSQSSAIGSAFIQDTRTIKTQSFQGRSSPQL

Parental  DPLRKSPTMEQAVQTASAHLPAPAPVGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDN
          DPLR.SPTMEQAVQTA.AHLPAPAPVGRRSPVST.PLPST.QK.IENQEH..AEV..VSR.ENEQLRN..
Retrocopy DPLRESPTMEQAVQTAPAHLPAPAPVGRRSPVSTPPLPSTGQKTIENQEHKQAEVPNVSRSENEQLRNHS

Parental  KRQVVPGASSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLE
          KRQVVPGASSAPR.GRGGHR.GR.RFGI.R.GPMKFE.DFDFE.ANAQFNKEEIDREFHNKLKLKEDKL.
Retrocopy KRQVVPGASSAPRKGRGGHRCGR-RFGIQRYGPMKFENDFDFERANAQFNKEEIDREFHNKLKLKEDKLQ

Parental  KQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETF
          K.EKPVNGE.KG...VDTQNSE...DEEDPLGPNCYYDK.KSFFDNIS...NRE.RPTWAEERRLNAETF
Retrocopy KKEKPVNGEGKG---VDTQNSEEDTDEEDPLGPNCYYDKSKSFFDNISYNINREQRPTWAEERRLNAETF

Parental  GIPLRPNRGRGGYRGRGGLGFRGGRGRGGGRGGTFTTPRGFRGGF----RGGRGGREFADFEYRK
          GIPL.PN.G.G.YR.R.GL.FRG.R...GGRGGTFTTPRGF..GF....R.G..GREFADFEYRK
Retrocopy GIPLHPNHGGGRYRSRRGLSFRGNRRPSGGRGGTFTTPRGFHWGFHRGFRRGHWGREFADFEYRK

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_170 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_170 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170 ,