RetrogeneDB ID: retro_itri_411

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:255580..256321(+)
• Located in intron of: ENSSTOG00000024448

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF9B
• Ensembl ID: ENSSTOG00000001982
• Aliases: None
• Description: TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa [Source:HGNC Symbol;Acc:17306]

Sequence

>retro_itri_411
ATGGAGTCTGGCAAGATGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAAATCCTGAAGGATATGGG
GATTACAGAATATGAGCCAAGAGTTATAAATCAGATGTTGGAATTTGCCTTCCGATATGTGACCACAATTCTAGATGATG
CTAAAATTTATTCCAGCCATGCTAAGAAAGCTACTGTTGATGCAGATGATGTGCGATTGGCAATCCAGTGTCGAGCTGAC
CAGTCTTTTACCTCTCCTCCCCCGAGAGATTTTTTATTAGATATTGCAAGGCAAAGAAATCAAACCCCTTTGCCATTGAT
CAAGCCATATTCGGGTCCTAGATTGCCTCCTGATAGATATTGCCTAACAGCTCCAAACTATAGGCTCAAGTCTTTACAAA
AGAAAGCATCTACTTCTGCAGGAAGAATAACAGTACCACGGTTAAGTGTTGGTTCAGTTACTAGCAGACCAAGTACTCCC
ACACTAGGCACACCAACCCCACAAACCATGTCTGTTTCAACTAAGGTAGGGACTCCAATGTCTCTAACAGGGCAAAGGTT
TACAGTACAAATGCCTACTTCTCAGTCCCCTGCTGTAAAAGCCTCAATTCCTGCAACATCAGCAGTTCAGAATGTTCTGA
TTAATCCATCATTAATTGGGTCCAAAAACATTCTTATTACTACTAATATGGTATCCTCACAAAATACTGCCAATGAATCA
TCAAATGCATTGAAAAGAAAA

Alignment

ORF - retro_itri_411 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.19 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESGKMAPPKNAPRDALVMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKPNVDADD
          MESGKMA.PK..P.DA..MAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKK..VDADD
Retrocopy MESGKMASPKSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDADD

Parental  VRLAIQCRADQSFTSPPPRDFLLDIARQKNQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSLIKKGS-NQ
          VRLAIQCRADQSFTSPPPRDFLLDIARQ.NQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSL.KK.S...
Retrocopy VRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYRLKSLQKKASTSA

Parental  GRL-VPRLSVGTVSSRPTTPTIA--TPQTVSVPNKVATPVSVTSQRFTVQIPPSQSTPVK-PVPATTAVQ
          GR..VPRLSVG.V.SRP.TPT....TPQT.SV..KV.TP.S.T.QRFTVQ.P.SQS..VK...PAT.AVQ
Retrocopy GRITVPRLSVGSVTSRPSTPTLGTPTPQTMSVSTKVGTPMSLTGQRFTVQMPTSQSPAVKASIPATSAVQ

Parental  NVLINPSMIGPKNILITTNMVSSQNTGNE-SNPMKRK
          NVLINPS.IG.KNILITTNMVSSQNT.NE.SN..KRK
Retrocopy NVLINPSLIGSKNILITTNMVSSQNTANESSNALKRK

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_411 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_411 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 28 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017613	1 retrocopy	retro_amel_449,
Bos taurus	ENSBTAG00000000895	1 retrocopy	retro_btau_196,
Canis familiaris	ENSCAFG00000017278	1 retrocopy	retro_cfam_192,
Callithrix jacchus	ENSCJAG00000019520	1 retrocopy	retro_cjac_246,
Cavia porcellus	ENSCPOG00000002098	2 retrocopies	retro_cpor_906, retro_cpor_967,
Equus caballus	ENSECAG00000010189	1 retrocopy	retro_ecab_303,
Erinaceus europaeus	ENSEEUG00000010916	1 retrocopy	retro_eeur_18,
Felis catus	ENSFCAG00000025493	2 retrocopies	retro_fcat_1036, retro_fcat_260,
Homo sapiens	ENSG00000187325	1 retrocopy	retro_hsap_2619,
Gorilla gorilla	ENSGGOG00000002470	2 retrocopies	retro_ggor_1833, retro_ggor_45,
Macropus eugenii	ENSMEUG00000009697	1 retrocopy	retro_meug_140,
Myotis lucifugus	ENSMLUG00000014581	1 retrocopy	retro_mluc_519,
Macaca mulatta	ENSMMUG00000012875	1 retrocopy	retro_mmul_1480,
Monodelphis domestica	ENSMODG00000004077	1 retrocopy	retro_mdom_850,
Mustela putorius furo	ENSMPUG00000000084	1 retrocopy	retro_mputfur_63,
Mus musculus	ENSMUSG00000047242	1 retrocopy	retro_mmus_161,
Nomascus leucogenys	ENSNLEG00000001378	5 retrocopies	retro_nleu_1677, retro_nleu_2566, retro_nleu_637, retro_nleu_920, retro_nleu_932,
Oryctolagus cuniculus	ENSOCUG00000014717	1 retrocopy	retro_ocun_490,
Otolemur garnettii	ENSOGAG00000011107	3 retrocopies	retro_ogar_1128, retro_ogar_3100, retro_ogar_679,
Pongo abelii	ENSPPYG00000020497	4 retrocopies	retro_pabe_1634, retro_pabe_2341, retro_pabe_2748, retro_pabe_941,
Pan troglodytes	ENSPTRG00000022053	4 retrocopies	retro_ptro_1329, retro_ptro_1765, retro_ptro_2145, retro_ptro_772,
Pteropus vampyrus	ENSPVAG00000017408	1 retrocopy	retro_pvam_6,
Rattus norvegicus	ENSRNOG00000002453	1 retrocopy	retro_rnor_1492,
Sus scrofa	ENSSSCG00000026714	2 retrocopies	retro_sscr_1080, retro_sscr_525,
Ictidomys tridecemlineatus	ENSSTOG00000001982	3 retrocopies	retro_itri_1640, retro_itri_411 , retro_itri_763,
Tarsius syrichta	ENSTSYG00000007968	1 retrocopy	retro_tsyr_3,
Tursiops truncatus	ENSTTRG00000015964	1 retrocopy	retro_ttru_572,
Vicugna pacos	ENSVPAG00000001210	1 retrocopy	retro_vpac_16,