RetrogeneDB ID: retro_itri_426

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:16891009..16892730(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIRC3
• Ensembl ID: ENSSTOG00000005734
• Aliases: None
• Description: baculoviral IAP repeat containing 3 [Source:HGNC Symbol;Acc:591]

Sequence

>retro_itri_426
ATGAAGTATGATTTTTCATGTGAGCTCTACAGAATGTCTACATATTCAACTTTCCCCATCAGTGTTCCTGTTTCAGAAAG
GAGTCTTGCTTGTGCTGGTTTTTATTACACTGGTGTGAATGACAAAGTCAGATGTTTCTGTTGTGGCCTGATGTTGGATA
ACTGGAAACAAGGAGATAGTCCTATTGAAAAGCATAAAGAGCTATAGCCTAGCTGCAGCTTTATTCAGAATTTGCTTTCA
GCTAGTCTGCAATCCACTTCTAAGAATACCTCTCCAATGAGAAACCATGTTGTACATTCATTATCTTCTAGTTTGGACCG
TAGTGGCTCATTCAGCGATTCTTATTCCTGCCTTTCACCAAATCCTCTTAATTCTAGAGCTGTTGAAGACTTCTCTCCAT
TGAGGACTAACCCCTATAGTTATGCAATGAGTACTGAAGAAGGCAGATTTCTTACTTATAATATGTGGCCCTTAACCTTT
TTGTCACCATTGGAATTGGCGAGAGCTGGCTTTTACTATGTAGGACCTGGAGATAGGGTAGCTTGATTTGCCCGTGGCGA
GAAGCTAAGTAACTGGGAACCAAAGGATGATGCTATGTCAGAACACAGGAGACATTTTCCCAACTGTCCGTTTTGGGAAA
ATTCTCTAGAAATGCTGAGGTTTAGTGTTTCAAATCTGAGCATGCAGACACACACAGCTTGAATGAGAACATTTATGTAC
TGGCCAGCTAGTGTTCCAGTTCAGCCTGAGCAGCTTGCAAGTGCTGGTTTTTATTACGTGGATCGTAATGATGATGTCAA
ATGCTTTTGTTGTGATGGTGGCTTGAGATGCTGGGAATCTGGAGATGATCTATGGGTAGAACATGCCAAATGGTTTCCAA
GGTGTGAGTTCTTGATACGAATGAAAGGGCAAGAGTTTGTTGATGAGATTCAAGCTAGATATCCTCATATTCTTGAAGAG
CTGTTGTCAACCTCAGATACTCCTGAGAAGAAAATGCTGAACAAATTGTTCATTTGGGACCTGGAGAAAGTTCTTCAGAA
GATGCAGTCATGATGAATACACCTGTGGCTAAATCTGCTTTGGAAATGGGTTTTAGTAGAAGTCTGGTAAAACAGACAGT
TCAAAGTAAAATCCTAACCATTGGAGAGAATTATTTAAAAAAAAAGTTAATGATATTGTATCAGCACTTCTTGATGCTGA
AGATGAAAGAAGAGGAGAAGGAAAGACAAGCTGAAGAAATGGCATCAGATGATTTGTCATTAATACGGAAGAATAGAATG
GCTCTCTTTCAACAGTTGACATGTGTCCTTCCTATCTTGGATAATCTTTTAAAGGCCAATGTAATTAATAAACAGGAACA
TGATATTATTAAACAAAAATCACAGATACCTTTACAAGCAAGAGAACTGATTGATACCATTTTAGTTAAAGGAAATGCTG
CAGCCAACATCTTCAAAAACTGTCTAAAGGAAATTGACTCTACATTATATGAGAACTTATTTGTGGAAAAGAATATGAAG
TATATTCCAACAGAAGATATTCCAGGTCTGTCACTAGAAGAACAGTTGAGGAGATTACAAGAAGAAAGAACCTGCAAGGT
GTGTATGGACAAAGAAGTTTCTATTGTGTTCATTCCTTGTGGTCATCTGGTAATATGCCAGGAGTGTGTCCCATCTCTAA
GAAAATTTCCTATTTGCAGGGGCATAATCAAGGGTAATCTA

Alignment

ORF - retro_itri_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.5 %
• Parental protein coverage: 95.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKYDFSCELYRMSTYSTFPSGVPVSERSLARAGFYYTGVKDKVKCFCCGLMLDNWKQGDNPIEKHKKLYP
          MKYDFSCELYRMSTYSTFP..VPVSERSLA.AGFYYTGV.DKV.CFCCGLMLDNWKQGD.PIEKHK.L.P
Retrocopy MKYDFSCELYRMSTYSTFPISVPVSERSLACAGFYYTGVNDKVRCFCCGLMLDNWKQGDSPIEKHKEL*P

Parental  SCSFVQNLNSVNNSKATSQPSFSSSVTNSTHSLLPSLENSGYFTGSYSSFLSNPVNSRANQDFSALRINP
          SCSF.QNL.S...S........S.......HSL..SL..SG.F..SYS....NP.NSRA..DFS.LR.NP
Retrocopy SCSFIQNLLSA--SLQSTSKNTSPMRNHVVHSLSSSLDRSGSFSDSYSCLSPNPLNSRAVEDFSPLRTNP

Parental  YHCSMNTEKARLLTYQMWPLTFLSPTELAKAGFYYIGPGDRVACFACGGKLSNWEPKDDAMSEHLRHFPN
          Y...M.TE..R.LTY.MWPLTFLSP.ELA.AGFYY.GPGDRVA.FA.G.KLSNWEPKDDAMSEH.RHFPN
Retrocopy YSYAMSTEEGRFLTYNMWPLTFLSPLELARAGFYYVGPGDRVA*FARGEKLSNWEPKDDAMSEHRRHFPN

Parental  CPFVENQFQDTSRYTVSNLSMQTHAARFKTFFNWPSSVLVHPEQLASAGFYYVGHSDDVKCFCCDGGLRC
          CPF.EN......R..VSNLSMQTH.A...TF..WP.SV.V.PEQLASAGFYYV...DDVKCFCCDGGLRC
Retrocopy CPFWENSLE-MLRFSVSNLSMQTHTA*MRTFMYWPASVPVQPEQLASAGFYYVDRNDDVKCFCCDGGLRC

Parental  WELGDDPWVEHAKWFPRCEYLIRIKGQEFVSQVQASYPHLLEQLLSTSDTPE-DENAESPIVHFGPGENH
          WE.GDD.WVEHAKWFPRCE.LIR.KGQEFV...QA.YPH.LE.LLSTSDTPE..ENAE..IVH.GPGE..
Retrocopy WESGDDLWVEHAKWFPRCEFLIRMKGQEFVDEIQARYPHILEELLSTSDTPE<EENAEQ-IVHLGPGESS

Parental  SEDAVMMNTPVVKAALEMGFSRNLVKQTVQSKILTAGENYKTISDLVLDLLNAEDEIREEAKERATEEKE
          SEDAVMMNTPV.K.ALEMGFSR.LVKQTVQSKILT.GENY.......L..........EE.KER..EE..
Retrocopy SEDAVMMNTPVAKSALEMGFSRSLVKQTVQSKILTIGENYXXXXLMILYQHFLMLKMKEEEKERQAEEMA

Parental  SGDLLLIRKNRMALFQHLTCVIPILDSLLIARVINEQEHDVIKQKTQTSLQARELIDTILVKGNTAATVF
          S.DL.LIRKNRMALFQ.LTCV.PILD.LL.A.VIN.QEHD.IKQK.Q..LQARELIDTILVKGN.AA..F
Retrocopy SDDLSLIRKNRMALFQQLTCVLPILDNLLKANVINKQEHDIIKQKSQIPLQARELIDTILVKGNAAANIF

Parental  KNSLQETDPMLYKHLFVQQDIRCIRTEDTSDLPMEEQLRRLQEERTCKVCMDKEVSIVFIPCGHLVVCKD
          KN.L.E.D..LY..LFV......I.TED...L..EEQLRRLQEERTCKVCMDKEVSIVFIPCGHLV.C..
Retrocopy KNCLKEIDSTLYENLFVEKNMKYIPTEDIPGLSLEEQLRRLQEERTCKVCMDKEVSIVFIPCGHLVICQE

Parental  CAPSLRKCPICRGTIKGTV
          C.PSLRK.PICRG.IKG..
Retrocopy CVPSLRKFPICRGIIKGNL

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_426 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_426 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000000608	3 retrocopies	retro_mdom_1857, retro_mdom_585, retro_mdom_683,
Ictidomys tridecemlineatus	ENSSTOG00000005734	1 retrocopy	retro_itri_426 ,