RetrogeneDB ID: retro_itri_564

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393301.1:9047499..9048199(-)
• 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_564
GTGAACATATTTGACTGGAAGATCCACTCTGTGCACTTTTAAATTTTTCACATATAATCCCTTGACCCAGCAGCATTCAA
AGAAGGTCTATGGCACTTTTGCCCTTCGTATGTTTCTGGTGGCTGCGGAAGCCTATGTCCTTGTGGTTACTCATTTCATT
CAGGCTGCCCTACTCTCTGCCTTGAGCTCCCTGGGGTTAATGATTTGGCTGATGTCAATACCTTATAGCTGTGAAACTGA
GCAGAAAACACTGGGACTTCTCACTGGATTTGCTTTCCTTACAGGAGTTGGTGTGCGCCCTGCCCTGGAATTGTGCATTG
ATGTCAATCTTAGCATCCTTCCCAGGCTTTCATGGGCACAGCAATTATCTTTACCTCCTTCACCCTCAATGCACTCTACA
CCAGGCACTACCTCTTTCTGGGAGGTATCTTGATGTCAGTCATGAGCCTGATGCTCTTGTCTTCACTGGGAAACCTTTTC
TTTGGATCCATTTGGCTTTTCCAGGCAAAACTGTATATGGGGCTGGTGGATGTGTTTGGCTTTGTCCTTTTTGATATTCA
ACTCATTATTGAAAAATGCTAAAAATGGCAATAAGGATTATATCTGGCACTGCATTGATCTCTTCTTCTATTTCATTACT
CTCTTCAGAGAACTCATGATGATCTGGGCTATGAATGAGAAAGACGAAAAGAAAGAGAAG

Alignment

ORF - retro_itri_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNIFDRKIN-FDALLKFSHI-TPSTQQHLKKVYASFALCMFLAAVGAYVHVVTHFIQAGLLSALGSLGLM
          .NIFD.KI....ALL.FSHI..P.TQQH.KKVY..FAL.MFL.A..AYV.VVTHFIQA.LLSAL.SLGLM
Retrocopy VNIFDWKIH<LCALLNFSHI<NPLTQQHSKKVYGTFALRMFLVAAEAYVLVVTHFIQAALLSALSSLGLM

Parental  IWLMATPHSHETEQKRLGLLSGFAFLTGVGLGPALELCIAVNPSILP-TAFMGTAMIFTCFTLSALYARR
          IWLM..P.S.ETEQK.LGLL.GFAFLTGVG..PALELCI.VN.SILP..AFMGTA.IFT.FTL.ALY.R.
Retrocopy IWLMSIPYSCETEQKTLGLLTGFAFLTGVGVRPALELCIDVNLSILP<QAFMGTAIIFTSFTLNALYTRH

Parental  RSYLFLGGILMSAMSLMLLSSLGNLFFGSIWLFQANLYVGLVIMCGFVLFDTQLIIEK-AENGDKDYIWH
          ..YLFLGGILMS.MSLMLLSSLGNLFFGSIWLFQA.LY.GLV...GFVLFD.QLIIEK.A.NG.KDYIWH
Retrocopy --YLFLGGILMSVMSLMLLSSLGNLFFGSIWLFQAKLYMGLVDVFGFVLFDIQLIIEK>AKNGNKDYIWH

Parental  CIDLFLDFVTLFRKLMMILAMNEKDKKKEK
          CIDLF..F.TLFR.LMMI.AMNEKD.KKEK
Retrocopy CIDLFFYFITLFRELMMIWAMNEKDEKKEK

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_564 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_564 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.

---

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,