RetrogeneDB ID: retro_itri_1293

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393429.1:1483036..1484346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERINC3
• Ensembl ID: ENSSTOG00000015682
• Aliases: None
• Description: serine incorporator 3 [Source:HGNC Symbol;Acc:11699]

Sequence

>retro_itri_1293
GTCCCCTGCCTCTGCAGTGGTGCACCATGCTTGCTGTGTAGTTGCTTTTCCAACATTAAGAAGTCCACTGGGACTTGGCT
CATCTATGCTTTTATTCTCCTCCTGAGAACTGCTGTGCTGACAGAAGGGACAGAAACTCAGATGACGAAGATTCCTGGAT
TCTGTGAAGGGTGATTTAAAATCAAGGTGGCTGATATAAAGGCAGATAAAGATTGGGATGTGCTGGTTTGTTATAAATCT
ATGTGTCAGATCAACTTTATCTTAGCCATTTTTGAGGGGGAGTTTCTTCTTTTTGCTCATGTTAAAAAATAAAAGCAAGT
AAAGCTCCCAGAGCAACAGTACATACTGGGTTTTTTTTTTATTCAAAATCGCTGCCATTGTTGGTATCACGATTGGATCT
TTCTACATCCCTGGGGGTACTTCACCTTGGCCTGGTTTGCTGTTGGTAAGGTGAGAGCTGCTTTGCTCATCCTCATCCAG
CTGGTACTCTTGGTAGACCTAGATAACCCTTGGAATGAATTATGGGTGAGTCGTATGGAAGAAAGAAACCCAAAGGTCTG
ATATGCCACTTTACTCTCTGATACAACCTTGTTTTATGTCCTGCCAATCGTCATTGTTGGGTTATTCCACACATACTACA
CTAAACCAGATGGCTGCACAGAAAACAAATTCTTCATCAATATTAATCTGATTCTCTGTGTTGTTTCCATTATATCCATC
CACCCCAAAATTCAGGAACATCAGCCTCGTTCAGGTCTCCTACAGTCCTCTGTCATCATGCTCTACACCTGTACCTCCCT
GGTCAGCCACGACAAATGAACTTGGTGGTTCCTGCAACCCTACTAAGAATCATTACACACATAAGTTCACTAACCATGGC
TCCTGCAAACTCCACTGCTGTAGTTCCTTTCTCTGCTCTGCCATCAAAGAAGAGGCACTTTCTGGATGTAGAAAATCTTC
TAGGGCTTACAGTCTTGGTTTCCTGTCTTTTGTATTCTAGCATTCGCTCTTCCAGCAACAGCCAAGTGAATAAGCTGACC
CCGCTCAGGGAGTGACAGCGTGATCCTTGATGATACAGCTGTCAGTGGAGCCAGCGATGAACAAGATGGACAGCCTTGGT
GGACTGTGAACAAGGAGAGAGAGGGAGTGCAGTACAGCTACTTGTTTTTCCATTTGATGCTCTGTTTGGCTTCCTTGTAC
GTCATGATGACACTGAATAGCTGGTATAGCTCTGATGCCAAATTCCAGAGTGTATCCAGCAAGTGGCCTGCTGTGTGGGT
CAAGATCAGCTCCAGCTGGGTGTGCCTCCT

Alignment

ORF - retro_itri_1293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 97.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VPCLCSGASCLLCSCCPNTKNSTVTRLIYAFILLLGTAVSCIMLTEGMETQLKKIPGFCEGGFKISVADI
          VPCLCSGA.CLLCSC..N.K.ST.T.LIYAFILLL.TAV....LTEG.ETQ..KIPGFCEG.FKI.VADI
Retrocopy VPCLCSGAPCLLCSCFSNIKKSTGTWLIYAFILLLRTAV----LTEGTETQMTKIPGFCEG*FKIKVADI

Parental  KADKDCDVLVGFKAVYRINFALAIFFFAFFLL-MLKVKTSKDPRAAVHNGFWF---FKIAAIVGIMVGSF
          KADKD.DVLV..K....INF.LAI.F...FLL..L..K.............W....FKIAAIVGI..GSF
Retrocopy KADKDWDVLVCYKSMCQINFILAI-FEGEFLL>LLMLKNKSK*SSQSNSTYWXXXXFKIAAIVGITIGSF

Parental  YIPGGS-FTSVWFVFGMVGAAFFILIQLVLLVDFAHSWNESWVSRMEEGNPRVWYAALLSVTTFFYVMSI
          YIPGG..FT..WF..G.V.AA..ILIQLVLLVD....WNE.WVSRMEE.NP.V.YA.LLS.TT.FYV..I
Retrocopy YIPGGT<FTLAWFAVGKVRAALLILIQLVLLVDLDNPWNELWVSRMEERNPKV*YATLLSDTTLFYVLPI

Parental  IVVGLFYTYYTKPDGCTENKFFISINLILCIVVSIIS-IHPKIQEHQPRSGLLQSSVITLYTLYLTWSAM
          ..VGLF.TYYTKPDGCTENKFFI..N..L...V..I..IHP..Q............V.....L.L.....
Retrocopy VIVGLFHTYYTKPDGCTENKFFI--NINLILCVVSII<IHPP-QNSGTSASFRSPTVLCHHALHLYLPGQ

Parental  TNEPDRSCNPTLLSIITHIASPTMTPANSTVVVPTSAPPSKKAHFLDAENLLGLAVFVFCLLYSSIRTSS
          ..........TLL.IITHI.S.TM.PANST.VVP.SA.PSKK.HFLD.ENLLGL.V.V.CLLYSSIR.SS
Retrocopy PRQMNLVVPATLLRIITHISSLTMAPANSTAVVPFSALPSKKRHFLDVENLLGLTVLVSCLLYSSIRSSS

Parental  NSQVNKLT-LSGSDSVILGDTNASGANDEEDGQPRRAVDNEKEGVQYSYSFFHLMLCLASLYIMMTLTSW
          NSQVNKLT..SGSDSVIL.DT..SGA.DE.DGQP...V..E.EGVQYSY.FFHLMLCLASLY.MMTL.SW
Retrocopy NSQVNKLT>RSGSDSVILDDTAVSGASDEQDGQPWWTVNKEREGVQYSYLFFHLMLCLASLYVMMTLNSW

Parental  YSPDAKFQNVTSKW-CC-VGQDHLQLGVPP
          YS.DAKFQ.V.SKW..C.VGQD.LQLGVPP
Retrocopy YSSDAKFQSVSSKW<ACCVGQDQLQLGVPP

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_1293 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1293 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
Mus musculus	ENSMUSG00000017707	1 retrocopy	retro_mmus_2372,
Ictidomys tridecemlineatus	ENSSTOG00000015682	1 retrocopy	retro_itri_1293 ,