RetrogeneDB ID: retro_itri_1154

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393388.1:4044874..4046139(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STAMBP
• Ensembl ID: ENSSTOG00000009888
• Aliases: None
• Description: STAM binding protein [Source:HGNC Symbol;Acc:16950]

Sequence

>retro_itri_1154
ATGTCTGACCATGGAGATGTGAGCCTCCCAGCCAAAGACAGGGTAAGGGCTCTGTTCCAGTTGGGAAGTACCGTGGAAGT
GAAGGAAGACATTCCACCCCCTCCATACTTCGCTCTGGAGTTGAGATGATCCCAATGGCATCCATTTACTCTGAGCAAGG
CAACATTGAACATGCCTTCATCCTCTATAACAAGTAAATCATGCTTTTTATTGAGAAACTACCAAAGCATCGAGATTATA
AATCAGCTGTTATTCCTGAAAAGAAAGATACAGTGAAGAAATTAAAGTAGATTGCATTTCCCAAAGCAGAACAGCTGAAG
GCAGAGCTGTTAAAACCATATACCAAAGAATATACACAGTATAATGAAGAAAAGAAGAAAAAAGCAGAGGGATTTGCCCA
GAATATGGCTATCCAGTAAGATTTGGAAAAGGAAAGACAGAGGATAGCACAGCAAAAGCAGCAACGGATGGAAAAGGAAG
AGTTCCATGCCTTTGAAAAAATGATCCAGAACCAGGAGCTAGAAAAAGAGCAACTGAAAATTGTACAGGAATTTGGGAAG
GTGGATCCTGGCCTAGGTGGCCCACTGGTGCCTGACTTGGAAAAGCCCTCCTTAGATGGGTTCCCCACCTCGCCTGTGTC
ATCCACACAGTCTTCAGACTGTAACACAACTTAAAGGCCAGCTAAGCCACCAGTGGTGGACAGATCCTTGGAACCTGGAG
CTCCAAGCAACACTGAGAGTATTCCTACAATCGATGGATTGCCTCATGTGGTGGTGCCCGGGAGGCTGTGTCTGCAGTTT
CTCCAGTTAGCCAGTGCCAACATGGCTCTGAGAGTACAAACGTGGAATTCTCTTGGAAAACTGAGGAGGAATGAATTTAC
CATTAGCCCTGTTCTCATCCCCAAGCAAACTGCTGGGTCTGATTATTGCAACACAGAGAATGAAGAACAACTTTTCCTCA
TACAGGATCAGCAGGGTCTCATTACACTGGGCTGGATTCATACCCATCCCACACAGACTACCTTTCTCTCCAGTGTCCAC
CTACACACTCACTGTTCCTACCAGATGCTGCTGCCAGAGTCAATAGCTATTGTCTGCTCCCCCCAAGTTTCAGGAAACTG
GATTCTTTCAATTAACTGACCATGGACTAGAAGAGATTTCTTCATGTCACCAGAAAGGATTTCATCCCCACAGCAAGGAT
CCACTCTGTTTTGTAGCTGTATCCACGTGACTGTTGTGGACAGAGCAGTGATTGTCACAGACCTT

Alignment

ORF - retro_itri_1154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.85 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDHGDVSLPPEDRVRALSQLGSTVEVNEDIPPRRYF-RSGVEMIRMASIYSEEGNIEHAFILYNKYITL
          MSDHGDVSLP..DRVRAL.QLGSTVEV.EDIPP..YF.RSGVEMI.MASIYSE.GNIEHAFILYNK.I.L
Retrocopy MSDHGDVSLPAKDRVRALFQLGSTVEVKEDIPPPPYF<RSGVEMIPMASIYSEQGNIEHAFILYNK*IML

Parental  FIEKLPKHRDYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYTQYNEEKKKKAEEFARNMAIQ
          FIEKLPKHRDYKSAVIPEKKDTVKKLK.IAFPKAE.LKAELLK.YTKEYTQYNEEKKKKAE.FA.NMAIQ
Retrocopy FIEKLPKHRDYKSAVIPEKKDTVKKLK*IAFPKAEQLKAELLKPYTKEYTQYNEEKKKKAEGFAQNMAIQ

Parental  QELEKERQRIAQQKQQQLEQEQFHAFEEMIRNQELEKERLKIVQEFGKVDPGLGGPLVPDLEKPSLDGFP
          ..LEKERQRIAQQKQQ..E.E.FHAFE.MI.NQELEKE.LKIVQEFGKVDPGLGGPLVPDLEKPSLDGFP
Retrocopy *DLEKERQRIAQQKQQRMEKEEFHAFEKMIQNQELEKEQLKIVQEFGKVDPGLGGPLVPDLEKPSLDGFP

Parental  TLPVSSTQPSDCNTTARPAKPPVVDRSLKPGALSNSESIPTIDGLRHVVVPGRLCPQFLQLASANTARGV
          T.PVSSTQ.SDCNTT.RPAKPPVVDRSL.PGA.SN.ESIPTIDGL.HVVVPGRLC.QFLQLASAN.A..V
Retrocopy TSPVSSTQSSDCNTT*RPAKPPVVDRSLEPGAPSNTESIPTIDGLPHVVVPGRLCLQFLQLASANMALRV

Parental  ETCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDL
          .T...L.GKL.RNEFTI..VLIPKQ.AGSDYCNTENEE.LFLIQDQQGLITLGWIHTHPTQT.FLSSV.L
Retrocopy QTWNSL-GKLRRNEFTISPVLIPKQTAGSDYCNTENEEQLFLIQDQQGLITLGWIHTHPTQTTFLSSVHL

Parental  HTHCSYQMMLPESIAIVCS-PKFQETGFFKLTDHGLEEISSCRQKGFHPHSKDP-PLFCSCTHVTVVDRA
          HTHCSYQM.LPESIAIVCS.PKFQETGFF.LTDHGLEEISSC.QKGFHPHSKDP..LFCSC.HVTVVDRA
Retrocopy HTHCSYQMLLPESIAIVCS>PKFQETGFFQLTDHGLEEISSCHQKGFHPHSKDP<TLFCSCIHVTVVDRA

Parental  VTVTDL
          V.VTDL
Retrocopy VIVTDL

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_1154 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1154 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000009888	1 retrocopy	retro_itri_1154 ,
Tursiops truncatus	ENSTTRG00000015478	1 retrocopy	retro_ttru_1858,