RetrogeneDB ID: retro_itri_1519

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393522.1:1723773..1724536(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLA
• Ensembl ID: ENSSTOG00000004771
• Aliases: None
• Description: galactosidase, alpha [Source:HGNC Symbol;Acc:4296]

Sequence

>retro_itri_1519
CTTGCTCTTTGCTCTATGTTCTCTGGGTGTCCTTGGGGCCAGGGCCTGGTGATGACACCTATCATGGGTTGCTTGCACTG
GGGGCACTTCCTGTGCGACCTTGACTGCCAGGAGGAGCCTGATTCCTGCACCAGTGAGCACCTCTTCATGCAGACGGCAG
AGGTCATGGTCTCCCACGGCTGGAAGAACACAGGTTCTGAGGACCTCTGCACTGGCCACTCTGGATAGCTCCCCAAAGAG
ACTGAAAAGTCACACTTCAGGGAGACCCTCAGTGCACTCGTGGTGGGAACTGCCGCCAAGCTGATTATGTCCATGGCAAA
GGGCCGAAGCCAGGGATCGATGCAGATGTTGGAAATGTAACCTGCAAGGTTTTTCTGGGAGCTTGGACACTGTGACATGA
TGCCCAGTCCTTGGCTGACTGGGAGCAGATTTGCAGAAGTGCCACCGCTGTCATGTGACCATGGGAAACATTTGCTAGAT
GGTCAGAAGCAGGTCACTGGCTCTGAACGGGACCAGCAAAAAGCATCGTATGCACCTGTGAGTGGCCCCTTTACACTGTA
CCCTGTCATGGTCCCAATTACACAGAAATCTGACAGCACTGTAATTACTGGAGAAATTCTACAAACATCTACAATTCCTG
GGAAAGTATATATGGCATCTTGACCTGAATAGCTTCTAACCAGGAAAGGATTGTTAATGTCGCTGGACCAGGGATTGGAA
TGACCCAGATAAGTTGGAGATGGGCAACTTTGGCCTCAGTTGG

Alignment

ORF - retro_itri_1519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 64.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LVLWGDFGAMALDNGLARTPTMGWLHWERFMCSVDCQEEPDSCISEQLFMQMAELMVSDGWKDAGYEYVC
          L.L...F.......GL..TP.MG.LHW..F.C..DCQEEPDSC.SE.LFMQ.AE.MVS.GWK..G.E..C
Retrocopy LALCSMFSGCPWGQGLVMTPIMGCLHWGHFLCDLDCQEEPDSCTSEHLFMQTAEVMVSHGWKNTGSEDLC

Parental  IDDC-WMAPQRNSLGQLQADPQRFPGGIRRLANYVHSKGLKLGIYADVGNKTCA-GYPGSF-GYYDI-DA
          .....W.APQR.....LQ.DPQ...GG..R.A.YVH.KG.K.GI.ADVGN.TC..G..GS..G..D..DA
Retrocopy TGHS<WIAPQRD*KVTLQGDPQCTRGGNCRQADYVHGKGPKPGIDADVGNVTCK<GFSGSL<GHCDM<DA

Parental  QTFAEW-GVDLLKFDGCHCDSIKHLADGYKYMSLALNRTGR-SIVYSCEWPLYMWPFHKPNYTKIRQYCN
          Q..A.W.G.DL.K...CH..............SLALN.T...SIV..CEWPLY..P.H.PNYT.I.Q.CN
Retrocopy QSLADW<GADLQKCHRCHV-TMGNIC*MVRSRSLALNGTSK>SIVCTCEWPLYTVPCHGPNYTEI*QHCN

Parental  HWRNFADVYDSWESVKSILDWTSSNQEKIVNFAGPG-GWNDPDMLVIGNFGLSW
          .WRN....Y.SWES...IL....SNQE.IVN.AGPG..WNDPD.L..GNFGLSW
Retrocopy YWRNSTNIYNSWESIYGILT*IASNQERIVNVAGPG<DWNDPDKLEMGNFGLSW

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_1519 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1519 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010267	1 retrocopy	retro_chof_1479,
Monodelphis domestica	ENSMODG00000011590	1 retrocopy	retro_mdom_204,
Oryctolagus cuniculus	ENSOCUG00000010859	1 retrocopy	retro_ocun_1190,
Ictidomys tridecemlineatus	ENSSTOG00000004771	1 retrocopy	retro_itri_1519 ,