RetrogeneDB ID: retro_itri_768

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393320.1:988279..988951(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024903
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CD9
• Ensembl ID: ENSSTOG00000001348
• Aliases: None
• Description: CD9 molecule [Source:HGNC Symbol;Acc:1709]

Sequence

>retro_itri_768
ATGCCAGTTAAAGGAGGTACCAAATGCATCAAGTACCTGTTCTTCGGATTTATCTTCATCTTCTGGCTTGCAGGAATTTC
AGTTCTTGCTATTGGACTATGGCTCCAATTCGACTCTCAGATCAAGAGCATCTTCCAGCAAGAAGCTAATAATTCCAACT
TCTACACAGGAGTTTGCATTCTGATTGGAGCTAGGGCCCTCATGATGCTGTGGGCTTCCTGGGCTGCTGTGGGGCCATGC
AAGAGTCCCAGTACATGTTGGGATTGTTCTTTGGCTTCCTCTTGGTGATATTTGCCACTGAAATAGCTGGAGCCATCTGG
GACTATTCACACAAGGATGAGGTGATTAAGGAAGTCCAGGACTTTTACACCTACAACAAGCTCAAGACCAAGAATGAGCC
CCAGTGGGAAATGCTGAAAGCCATCCACCATGCGTTGAACTGCTGTGGTATAGTTGGAGGTGTTGAACAGTTTATCTTGG
ACATCTGCTCCCAAAAAGGACATTGTCAAAACCACCCAAATTAAGTCCTGCCCTGCGGCCATCAAAGAGGTCTTCAATAA
CAAGTTCCACATCATTGGTGCAGTGGGCATCCGCATCTCAGTGGTGATGATATTTGGCATGATCTTCAGTATGATCTTGT
GCTGTGCTATCCGCAGGAGCAGCAAGATGATC

Alignment

ORF - retro_itri_768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPVKGGTKCIKYLLFGFNFIFWLAGIAVLAIGLWLRFDSQTKSIFEQEANHSSFYTGVYILIGAGALMML
          MPVKGGTKCIKYL.FGF.FIFWLAGI.VLAIGLWL.FDSQ.KSIF.QEAN.S.FYTGV.ILIGA.ALMML
Retrocopy MPVKGGTKCIKYLFFGFIFIFWLAGISVLAIGLWLQFDSQIKSIFQQEANNSNFYTGVCILIGARALMML

Parental  -VGFLGCCGAVQESQCMLGLFFGFLLVIFAIEIAAAIWGYSHKDEVIKELQDFYKDTYNKLKTKDEPQRE
          .VGFLGCCGA.QESQ.MLGLFFGFLLVIFA.EIA.AIW.YSHKDEVIKE.QDFY..TYNKLKTK.EPQ.E
Retrocopy <VGFLGCCGAMQESQYMLGLFFGFLLVIFATEIAGAIWDYSHKDEVIKEVQDFY--TYNKLKTKNEPQWE

Parental  TLKAIHYALNCCGVVGGVEQFILDIC-PKKDIIETIQIKSCPEAIKEVFDSKFHIIGAVGIGIAVVMIFG
          .LKAIH.ALNCCG.VGGVEQFILDIC.PKKDI..T.QIKSCP.AIKEVF..KFHIIGAVGI.I.VVMIFG
Retrocopy MLKAIHHALNCCGIVGGVEQFILDIC>PKKDIVKTTQIKSCPAAIKEVFNNKFHIIGAVGIRISVVMIFG

Parental  MIFSMILCCAIRRSREMV
          MIFSMILCCAIRRS..M.
Retrocopy MIFSMILCCAIRRSSKMI

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_768 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_768 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009313	1 retrocopy	retro_eeur_174,
Felis catus	ENSFCAG00000006863	1 retrocopy	retro_fcat_1098,
Myotis lucifugus	ENSMLUG00000006901	1 retrocopy	retro_mluc_2384,
Monodelphis domestica	ENSMODG00000018053	3 retrocopies	retro_mdom_1490, retro_mdom_226, retro_mdom_872,
Mus musculus	ENSMUSG00000030342	1 retrocopy	retro_mmus_3022,
Ictidomys tridecemlineatus	ENSSTOG00000001348	1 retrocopy	retro_itri_768 ,