RetrogeneDB ID: retro_itri_59

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393790.1:380585..382088(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021919
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSSTOG00000000714
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_itri_59
ATGGGGATCCTAAGTAGCAGGATCTTGCGATGCAGAGAACCAGGTACCATAGATCTGCAGCAGTCTGAAGCCACAGCGGG
TCCCAGTTACATATCTAGCAGTCGGAAGCGTAAGCAGAGTGGTGGGTATTGTTCAGGTTTAAAATCTGACACCAAGAAGT
TTCAGGACCAGGGAGAAAATCTACAGCAAGTCTTCAGCACCAACCACAGAAAAAAAGTTAAGATTACATCCAAGTATGCT
TACCAAAATTTATTTTTGAATGGAGAAAACAGTGACATCAAAATCCGTGCTCTGGGGAAAATATGGTGTTTACACAAAAT
ATTTTTATATCAATCAGACTACTTTGCTGATATGTTTAGAAGTTCTTGGGAAGAATTGCACAAAGATATTATTGAACTGG
ATATTCGTGACCAGAATATAGATATCCAATCTTTGCACTTTGTACTAGGTTCATTGTATAGGGATGAGTATTTCTTAATA
GAGCCCCTTCAAGTTCCAGGTGTTTTGGCAACATCATATCTGCTTCAGGTAGAGGACTTAATTCAGCAATGTAGTGAAAC
CATGAAAGACACAATTAATGTGAAAACTGTATGTAGTTATTATGCAGCAGCAGAAACCTATGGGTTAGATTCTGTAAAGA
CAGGGTGCTTTGAATGGCTTCTTCACAATTTGATGACACACCCAAGTGCTGAGCTCTACAAAGAAATAGGCATAGAGCTT
ATGGATTTGCTCATCTCTTCCTCTAATTTACTAGTAATACAAAAGGAAATGGATATATACACAACACTTAAAGAGTGGAT
GTTTCTTCATCTTAACCCATCTTGGAAAGGCTCAATGAAACAGCTTCTAATTAATACTAATAATTGGCTTTCTAGACACA
GGGAATGTGGTGGCTATAACACTTTTCTTGACACAGAAGAAGGAATATCATTTAAACCAGTGTTTAAAAAATTGAGGTTT
CAGCATATCATCTGTGACCTGGCCTCAACAAAAGTAATTGAACAAGATGGTCTAATACCTTCAGAGTGGTTGTCATCTGT
TTACAAACAACAATGGCTTACCTTGCTTAAGGCACAACAATACAGGGAGATCGGGCCTCGAGACATCAATGAAACAGAAC
TTGAAGGATACAGCATGAGGTGTGGTAAAAGGATTATCAAAGATGGTAAATATTCCTGGAAGTGGTCAGGTTACAATTTT
GGCTTTCCCTTACATGTTATTTTTGACAGCCATTATATAATTTTCAAGCAAAATACTTTCAGTCAGCTATGTGAAGATTC
TGCCTGCTTACAACCTCTACGAAATATTGCGTTCAGATTAACTTTGGTATATTTTGATGCTAGTGGAAAATTAAATTTCA
GCAAAACAACAGGCTATAAAATACTTACTTTTTCAAAAGATGAGGAACAAGTGGTGATGAAGTTGGATAGCATAGTTCTG
AACTTCCCTTTATATATATTCTGCAACTTCCTATTTATATCATTAGAAAATACAGAAAACTGA

Alignment

ORF - retro_itri_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.79 %
• Parental protein coverage: 89.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YCPGSRKRKRSSGAFCYCHP-DSETDEDEDEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKIC
          Y...SRKRK.S.G...YC....S.T....D.G...Q....T..RKK.K.TSKY.YQ.LFLNGENSDIKI.
Retrocopy YISSSRKRKQSGG---YCSGLKSDTKKFQDQGENLQQVFSTNHRKKVKITSKYAYQNLFLNGENSDIKIR

Parental  ALGEEWSLHKIYLCQSGYFSSMFSGSWKESSMNIIELEIPDQNIDIEALQVAFGSLYRDDV-LIKPSRVI
          ALG..W.LHKI.L.QS.YF..MF..SW.E....IIEL.I.DQNIDI..L....GSLYRD...LI.P..V.
Retrocopy ALGKIWCLHKIFLYQSDYFADMFRSSWEELHKDIIELDIRDQNIDIQSLHFVLGSLYRDEYFLIEPLQVP

Parental  AILAAACMLQLDGLIQQCGETMKETINVKTVCGYYTSAGIYGLDSVKKKCLEWLLNNLMTHQNVELFKEL
          ..LA....LQ...LIQQC.ETMK.TINVKTVC.YY..A..YGLDSVK..C.EWLL.NLMTH...EL.KE.
Retrocopy GVLATSYLLQVEDLIQQCSETMKDTINVKTVCSYYAAAETYGLDSVKTGCFEWLLHNLMTHPSAELYKEI

Parental  SINIMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTETDVWFSKRRKDFEGTAFLETE
          .I..M..LI.SSNL.V.Q.EMD.YT.LK.WMFL.L.PSW.GS.KQLL..T..W.S..R.......FL.TE
Retrocopy GIELMDLLISSSNLLVIQKEMDIYTTLKEWMFLHLNPSWKGSMKQLLINTNNWLSRHRECGGYNTFLDTE

Parental  QGKPFVSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLAMLRAEQDSEVGPQEINKEELEG
          .G..F..VF..LR.Q.II.DLAS...IEQD.L.PSEWLSSVYKQQWL..L.A.Q..E.GP..IN..ELEG
Retrocopy EGISFKPVFKKLRFQHIICDLASTKVIEQDGLIPSEWLSSVYKQQWLTLLKAQQYREIGPRDINETELEG

Parental  NSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFD
          .SMRCG....KDG.Y.W.W.G.NFGF.L.V.....YIIFK.NT..Q.C..S..LQP.R.IAFRL.L..FD
Retrocopy YSMRCGKRIIKDGKYSWKWSGYNFGFPLHVIFDSHYIIFKQNTFSQLCEDSACLQPLRNIAFRLTLVYFD

Parental  SSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYISPEKRTEN
          .SGKL..S.TTGY.ILT..KD.EQVVM.LDS..L.FPLYI.CNFL.IS.E..TEN
Retrocopy ASGKLNFSKTTGYKILTFSKDEEQVVMKLDSIVLNFPLYIFCNFLFISLE-NTEN

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_59 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_59 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59 ,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,