RetrogeneDB ID: retro_itri_1226

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393407.1:601450..602222(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DLD
• Ensembl ID: ENSSTOG00000007445
• Aliases: None
• Description: dihydrolipoamide dehydrogenase [Source:HGNC Symbol;Acc:2898]

Sequence

>retro_itri_1226
GTCAGAATTGATATGAAGGTATCTAAAAACATTCAAAGAATCCTTCAAAACCAAGGGTTTAAGTTTAAGTTGAATATAAA
GGTTACTGGTGTTACCAAAAAAGTCATATGGAAAAATTATGTTTCTATTGAAGCTGCTTCTGGTGGTAAAGCTGAAGTTA
TCACTTTTGTGTACTCTTGGTTTGCATTGGTCGACAACTCTTTACTCTAAATTTTGGACTAGAAGAGATTGGATTGAAAC
AGGTCTCAGAGGAAAAATTCCAGTCCATAACAGATTCCAAACAAAAATTCCAAATGTCTATGCTATTGGTGATATGGTTG
CTGGTCCCATGCTGGCTCACAAAGCAGAGGATGAAGCCATTATGAGTGTTAAAGGAATGGCTGGGGTGCTGTGTACACTG
ACTACAATTGTGTGCCATTGCTGATTTACAGACACCCCAAAGTTGCATGGGGCAAATCAGAAGAGCAGTTGGAGAAAGAG
GATATCGAGTACAAAGTCGGAAAATTTCCCTTTGCTGCTAACAACAGAGCTAAGACAAATGTTGACACAGATGGCATGAT
GAAGATTCTTAAGCAGAAATCAATGAACCAAATACTGGGAGCACATATTCTAGGACCAGGTGCTGGAGAAATGGTAAATC
AAGCTGTTTTGGCTTTGGAATATGAAGCCTCCTGTGAAGATACAGCTAGAGTCTGCCATGTGCATCCAACCATATTAGAA
GCTTTTAGAGAAGCAAATCTGGCTGCATCATTTGGCAAATCAATCAACTTTT

Alignment

ORF - retro_itri_1226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.05 %
• Parental protein coverage: 50.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VGIDMEVSKNFQRILQKQGFKFKLNTKVTGATKKSDGKIDVSIEAASGGKAEVITCD-VLLVCIGRRPFT
          V.IDM.VSKN.QRILQ.QGFKFKLN.KVTG.TKK...K..VSIEAASGGKAEVIT...VLLVCIGR..FT
Retrocopy VRIDMKVSKNIQRILQNQGFKFKLNIKVTGVTKKVIWKNYVSIEAASGGKAEVITFV<VLLVCIGRQLFT

Parental  QNLGLEDLG-IELDPRGRIPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGIAG-GAVHIDYN
          .N.GLE..G.IE...RG.IPV..RFQTKIPN.YAIGD.VAGPMLAHKAEDE.I..V.G.AG.GAV..DYN
Retrocopy LNFGLEEIG<IETGLRGKIPVHNRFQTKIPNVYAIGDMVAGPMLAHKAEDEAIMSVKGMAG<GAVYTDYN

Parental  CVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILG
          CVP..IY.HP.VAW.GKSEEQL..E.IEYKVGKFPFAAN.RAKTN.DTDGM.KIL.QKS....LGAHILG
Retrocopy CVPLLIYRHPKVAW-GKSEEQLEKEDIEYKVGKFPFAANNRAKTNVDTDGMMKILKQKSMNQILGAHILG

Parental  PGAGEMVNEAALALEYGASCEDIARVCHAHPTLSEA-LEKQTWLHHLANQSIF
          PGAGEMVN.A.LALEY.ASCED.ARVCH.HPT..EA.LEKQ.WLHHLANQS.F
Retrocopy PGAGEMVNQAVLALEYEASCEDTARVCHVHPTILEA>LEKQIWLHHLANQSTF

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_1226 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1226 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005312	1 retrocopy	retro_cpor_685,
Monodelphis domestica	ENSMODG00000016316	2 retrocopies	retro_mdom_1455, retro_mdom_448,
Oryctolagus cuniculus	ENSOCUG00000014667	1 retrocopy	retro_ocun_437,
Ictidomys tridecemlineatus	ENSSTOG00000007445	1 retrocopy	retro_itri_1226 ,
Tursiops truncatus	ENSTTRG00000003989	1 retrocopy	retro_ttru_699,