RetrogeneDB ID: retro_itri_1273

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393422.1:971633..972284(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMBIM6
• Ensembl ID: ENSSTOG00000001165
• Aliases: None
• Description: transmembrane BAX inhibitor motif containing 6 [Source:HGNC Symbol;Acc:11723]

Sequence

>retro_itri_1273
TTAAAAATTTCACATACTATCTTGAGACAGTAACCCTTGAAGGAGGTCTATGCCAAATTTTCCCTTTGTATGTTTTTGGG
GATTATGGGGCCTGTGTTTATGTGGGCACTCATTTCATTCACGTGGATCTGCTCTTTGTGTTGGGGTCCCTGGGATTTTA
ATGATTTGGCTGATGGGAACACATTGAAACTGTGAAAATGAGCAGAAAAGACTGGGACTTCAGGTCAGATTTGCTCTTCT
TACAGGAGCTGGCCTGAGCGCTGCTCAGCTGTGCATTGCTGTCAATCCCAGCATCCTTCCCAGGCCTTCATGGGCATAGC
AATGGTCTTCACCTGCTTCCCCCTGAGTGCACTTTGGGCCAGGCACCTCTTTCTGGGAGGTATCTTGATGTCAGACATAG
CCTGATGATTTGGTCTTCCCTGGGGAAACTTTCCTTTGGATCCATTTGGCTTTTCCAGGCAAAACTCCATAGGGGCTAGT
GGTCATGTGCGACTTTGCCCTTTTTGATAATCAACTCATTATTGAAAAAGCTGAAAATGTCAATAAGGATTATATCTGGC
ACTGTGTTGATCTCTTCTTAGATTTTGTTATTCTCTTCCAAAAATTCATGATGATTTCTGGCTATAAAAAAAAGACAAAA
TGAAAGAGAAG

Alignment

ORF - retro_itri_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.35 %
• Parental protein coverage: 94.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LKFSHITPSTQQHLKKVYASFALCMFLAAVG-AYVHVVTHFIQA-GLLSALGSLG-LMIWLMATPHSHET
          LK.SH.T...Q..LK.VYA.F.LCMFL...G.A.V.V.THFI...G.....G..G.LMIWLM.T....E.
Retrocopy LKISH-TILRQ*PLKEVYAKFSLCMFLGIMG<ACVYVGTHFIHV<GSALCVGVPGILMIWLMGTH*NCEN

Parental  EQKRLGLLSGFAFLTGVGLGPALELCIAVNPSILPT-AFMGTAMIFTCFTLSALYARRRSYLFLGGILMS
          EQKRLGL...FA.LTG.GL..A..LCIAVNPSILP..AFMG.AM.FTCF.LSAL.AR....LFLGGILMS
Retrocopy EQKRLGLQVRFALLTGAGLSAA-QLCIAVNPSILPR<AFMGIAMVFTCFPLSALWAR---HLFLGGILMS

Parental  AM-SLMLLSSLGNLFFGSIWLFQANLYVG-LVIMCGFVLFDTQLIIEKAENGDKDYIWHCIDLFLDFVTL
          ...SLM..SSLG.L.FGSIWLFQA.L..G.LV.MC.F.LFD.QLIIEKAEN..KDYIWHC.DLFLDFV.L
Retrocopy DI<SLMIWSSLGKLSFGSIWLFQAKLHRG<LVVMCDFALFDNQLIIEKAENVNKDYIWHCVDLFLDFVIL

Parental  FRKLMMILA-MNEKDKKKEK
          F.K.MMI.......DK.KEK
Retrocopy FQKFMMISG<LXXXDKMKEK

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_1273 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1273 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018588	1 retrocopy	retro_btau_762,
Canis familiaris	ENSCAFG00000008400	2 retrocopies	retro_cfam_1220, retro_cfam_876,
Callithrix jacchus	ENSCJAG00000021032	1 retrocopy	retro_cjac_272,
Dasypus novemcinctus	ENSDNOG00000007882	2 retrocopies	retro_dnov_164, retro_dnov_857,
Macropus eugenii	ENSMEUG00000015590	4 retrocopies	retro_meug_1076, retro_meug_1706, retro_meug_2157, retro_meug_48,
Monodelphis domestica	ENSMODG00000004277	2 retrocopies	retro_mdom_210, retro_mdom_250,
Otolemur garnettii	ENSOGAG00000005137	2 retrocopies	retro_ogar_1074, retro_ogar_3470,
Pteropus vampyrus	ENSPVAG00000016821	1 retrocopy	retro_pvam_755,
Sarcophilus harrisii	ENSSHAG00000010366	1 retrocopy	retro_shar_622,
Ictidomys tridecemlineatus	ENSSTOG00000001165	2 retrocopies	retro_itri_1273 , retro_itri_564,
Tarsius syrichta	ENSTSYG00000002427	1 retrocopy	retro_tsyr_916,