RetrogeneDB ID: retro_itri_1807

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393844.1:239546..239988(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSSTOG00000006720
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:10781]

Sequence

>retro_itri_1807
ATGATCCACAGTGGAGAGCAGAACTATGGCCACCATGAATCCCATTCTCCTTTCAGAAGTGTAAGTGCTCATAGATCAGG
GAAATCTGTAAGGCAAATCCTTGCATGATCTTAGTCCAAGGCAGTTTGCAGATATTCCAGATCAAAGTTCAGGTCAGATC
TGAATCTAGGTCTAGATTCAGAAGAAGATTTCAAAGGCATTATGCAAGGCTGTGGTCTTGATTTAACTCCCAAATAAGCT
CCTCTATCAGGTTTACAGTCAATATTATCACAGAAGGCACAGTCACAGTCAATCTGCCATGTCTACCGGAGGACCTCACA
TGGACAATCCAACAAATCCTGACCAAAACTGTTGTCTTGGAGTGTTTGGGTTGAACTGGTATACTATGGAAAGAAATCTA
AAAGAAGTGTTTTCTAAATATGGACCTATTGCTGGTGTGTCT

Alignment

ORF - retro_itri_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62. %
• Parental protein coverage: 51.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRS-RSESRSRSRRSSRRHYT
          M..SGEQNYG..ES.S..RS.SAH.SGKS.R...A.S.SK...R.SRSK.RS.RSESRSR.RR...RHY.
Retrocopy MIHSGEQNYGHHESHSPFRSVSAHRSGKSVRQILA*S*SKAVCRYSRSKFRS<RSESRSRFRRRFQRHYA

Parental  RSRSRSRSHRRSRSRS-YSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVF
          R..S...S...S..R..YS..Y.RRHSHS.S.MST...H..N..NPD.NCCLGVFGL..YT.ER.L.EVF
Retrocopy RLWS*FNSQISSSIRF<YSQYYHRRHSHSQSAMSTGGPHMDNPTNPDQNCCLGVFGLNWYTMERNLKEVF

Parental  SKYGPIADVS
          SKYGPIA.VS
Retrocopy SKYGPIAGVS

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_1807 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1807 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000010611	3 retrocopies	retro_mmur_1102, retro_mmur_1135, retro_mmur_1410,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Ictidomys tridecemlineatus	ENSSTOG00000006720	2 retrocopies	retro_itri_1807 , retro_itri_776,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,