RetrogeneDB ID: retro_itri_160

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:26880536..26882702(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024488
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LETM1
• Ensembl ID: ENSSTOG00000014167
• Aliases: None
• Description: leucine zipper-EF-hand containing transmembrane protein 1 [Source:HGNC Symbol;Acc:6556]

Sequence

>retro_itri_160
ATGGCATCCATTCTTCTGAGGAGCCCTGGCAGCTGGGCACCCGCCCGCTTCCCCATGCCCGTCGCCGCAGCGTGGGACGG
TGGCCTGGGGGACGGTCCCACGTACCAACACCGTACCAACACCGTTGGGCTGGTCAGCCGCATGGATGCGCCATTTGGCT
GCTGCGCTCGTGTCCACTCATTGTACCGCTCCTTCAGAGGCCATTGCTTCCACAGCTGGCCTCTGAGGCCCGAGCGCTTG
CACACGGTGGCATCCGCCCCGCGTTTGGTTGTCATAGGACCTGGGGACCTTCCTGTGCGCTGCTGGCACTCGTCGTACCC
CCTCAGCAGTAACTCCACAGTGACATCTCCCAAGTCCCTCAGGGACAAGAATAAGAAGCTAGAGGAAGGTAGCCCTGTGT
CCAACACCACCGCGGAGCGGGCAGTGAAGCCTGGCCTCAAGCAGAGGATCCTAGACGGGCTGAAGCACGTTTACCACGGC
TTCCGCCTGCTCTGGATCGACACCAAGATCGCTGTGCGCACGCTCTGGAAGATTCTCAAGGGCCAGACCCTGAGCCGCAG
GGAGCATAAGCAGTTAGTTCGGGTCTGCGCTGACCTCTTCCGCCTTGTACCACTCCTTGCCTTTGTGGTAGTGCCATTCA
TGGAGTTTCTGCTACCCATTGCCCTCAAACTCTTTCCCAACATGTTGCCATCCACGTTTGAGACACAATCTATCAAGGAA
GAGAAGCTGAAAAAGAAGCTGCGGGTCAAGCTGGAGCTGGCCAAGTTCCTACAGGACACTGCTGAGGAGATGGCCTCTAG
GAACAAGGCAGCCACCGGGAGCACTGCCAAAGACTTCTCCCAGTTTTTCCAGAAGATCAGAGAAACTAATGAAAGACCTA
GCAATGAGGAAATCGTGCGTTTTTCCAGGTTGTTTAAGGATGAGCTGACCCTGGGTAACCTGCCCCGGCAGCAGCTGATG
GCTCTGTGTAAGCTGCTGGGACTCCAGGCCATTGGCACCAACAGCTTCCTACGCTTCCAGATTACCATGCAGCTGAGGTC
CATAAAGGCTGATGACGAGCTGATTGCTAAAGAAGGGGTAGACAGCCTGAATGTCACGGAGTTGCAATCAGCCTGTCGGG
AGAGAGGCATGCCTGTCCTGGGTGTCACAGAAGATCGGCTGAGGGACCAGCTGAAGCAGTGGCTGGACTTGCACCTGCAC
CAAAAGATCCCCACTTCACTACTTATATTATCTCAAGCTATGTATTTCCCAACCACCTTCTCTCCTACTGACCAGCTCAC
ATCCACACTGCAGAAGCTTCCAGAGACTGTGGTGAAGGGAGCCCAGGTTCAAGTGGCCAATGTTAAAGGCAGTCAGGTGG
ACAACAAGATGAAGCTAGAGGCCACGCTGCAGGAGGAGGCAGCCATCCAACAGGAGCACTGGGAGAAGGAACTACAGATG
CTGTCCCAAGCAGTGGTAGAAGACACCTCTGGGAGGCCAATGGCTGACCAGCAGCTGGAAGTGTCAGATAGGAGTCTGCC
ATCAGAGTCCCATCTCATTGCCCCTGTGGTTGAGGTGTTGAAGGAAGAGGAAATAACTAAGGAAGAAATCCACATACTCA
GCAGTGCCTGTTCTCAACTGAAGGAGCAGAGGAAGTCCCTATCCAAGGAGAAAGAAGAGCTTGAACTGCTGAAGGAAGAT
GTCCAGGACCACAGTGAGGACTTACTAGAGATCAAGAAGGAACTTTTGAAGACTGGTGGAAAAAAACATGTGGAAGCACC
TAAAGCCAGCCAGAGGGTAAAAAAGAGAGTCCAGCAGATGATTGGACAGATACACAGCTTGATCTTGCAGCTGGAGACAG
ACCAGAAGGCTGGCAAGCTAGAGCCAGCAAAGGGCTCACTCACAGGGACAGAAATTGTCAGTATCACTGAGCTCGCCAGT
GCCCTGAAGCAAATCAAGCACATTCCAGAAACTAAGCTGATCCACTTGGCCTCAACATTTGATAAGAATAAGGATGGCAA
GATCAACATTGACAAATTCATGAATATGGTTGAGCTGATAGACAAAGAAGACATTGACATCCCCACCAGCCAGGTGGCCA
CAGTTTTGGCAATGCTGGAAAAGGAGGAGATGATAAAGAAGGCCAAAGAAAGGGCTGAGAAGGAGGCTGCAGGAGTGAAG
GCTTAG

Alignment

ORF - retro_itri_160 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.82 %
• Parental protein coverage: 55.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRTAVRVPWTPTSAGLVVTGPRYLSMRGWHSSPPLSDDSVVEKSLKSLKDKNKKLEEGGPVYSPPAEVVV
          P....R.........LVV.GP..L..R.WHSS.PLS..S.V..S.KSL.DKNKKLEEG.PV....AE..V
Retrocopy PLRPERLHTVASAPRLVVIGPGDLPVRCWHSSYPLSSNSTVT-SPKSLRDKNKKLEEGSPVSNTTAERAV

Parental  KKSLGQKVLDELKHYYHGFRLLWIDTKIAARMLWRILNGHTLTRRERRQFLRICADLFRLVPFLVFVVVP
          K..L.Q..LD.LKH.YHGFRLLWIDTKIA.R.LW.IL.G.TL.RRE..Q..R.CADLFRLVP.L.FVVVP
Retrocopy KPGLKQRILDGLKHVYHGFRLLWIDTKIAVRTLWKILKGQTLSRREHKQLVRVCADLFRLVPLLAFVVVP

Parental  FMEFLLPVAVKLFPNMLPSTFETQSIKEERLKKELRVKLELAKFLQDTIEEMALKNKAAKGNATKDFSAF
          FMEFLLP.A.KLFPNMLPSTFETQSIKEE.LKK.LRVKLELAKFLQDT.EEMA..NKAA.G...KDFS.F
Retrocopy FMEFLLPIALKLFPNMLPSTFETQSIKEEKLKKKLRVKLELAKFLQDTAEEMASRNKAATGSTAKDFSQF

Parental  FQKIRETGERPSNEEIMRFSKLFEDELTLDNLTRPQLVALCRLLELQSIGTNNFLRFQLTMRLRSIKADD
          FQKIRET.ERPSNEEI.RFS.LF.DELTL.NL.R.QL.ALC.LL.LQ.IGTN.FLRFQ.TM.LRSIKADD
Retrocopy FQKIRETNERPSNEEIVRFSRLFKDELTLGNLPRQQLMALCKLLGLQAIGTNSFLRFQITMQLRSIKADD

Parental  KLIAEEGVDSLNVKELQAACRARGMRALGVTEERLRGQLKQWLDLHLHHEIPTSLLILSRAMYLPDTLSP
          .LIA.EGVDSLNV.ELQ.ACR.RGM..LGVTE.RLR.QLKQWLDLHLH..IPTSLLILS.AMY.P.T.SP
Retrocopy ELIAKEGVDSLNVTELQSACRERGMPVLGVTEDRLRDQLKQWLDLHLHQKIPTSLLILSQAMYFPTTFSP

Parental  ADQLKSTLQTLPEIVAKEAQMKVAEVEGEQVDNKVKLEATLQEEAAIQQEHREKELQRAAEA
          .DQL.STLQ.LPE.V.K.AQ..VA.V.G.QVDNK.KLEATLQEEAAIQQEH.EKELQ....A
Retrocopy TDQLTSTLQKLPETVVKGAQVQVANVKGSQVDNKMKLEATLQEEAAIQQEHWEKELQMLSQA

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_160 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_160 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001859	1 retrocopy	retro_cjac_1529,
Homo sapiens	ENSG00000168924	1 retrocopy	retro_hsap_2019,
Gorilla gorilla	ENSGGOG00000002923	2 retrocopies	retro_ggor_1158, retro_ggor_1159,
Nomascus leucogenys	ENSNLEG00000000067	2 retrocopies	retro_nleu_1752, retro_nleu_2731,
Otolemur garnettii	ENSOGAG00000014883	1 retrocopy	retro_ogar_20,
Pongo abelii	ENSPPYG00000014533	1 retrocopy	retro_pabe_1655,
Ictidomys tridecemlineatus	ENSSTOG00000014167	1 retrocopy	retro_itri_160 ,