RetrogeneDB ID: retro_itri_1119

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393380.1:652514..653086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSSTOG00000015326
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_itri_1119
GCCATCACTCAGTTTCGGCTAATTTAAAGTTTGTACCTGCCTAGCACAGTGTTCTCAGTCCTAAAGAGATTAATATGCAG
ATCTGGCAAAGGAAGTAAATTAAGTGGAGACCAAATAACTCTGCCAACTACAGGTGATTACCCATCAGTTCCTAAGCAGA
CTGATGTGGAAGAGGGGCTTCCTGGGATGAGGATGCACCCACAGTGCGAAGGCTAAAGGCGGGAATGGAAAGGTGGCCGC
ACAACAAAATGCTTTGGAACAAATGGAACCTGACTACTTTAAGGGCATGACACCAACTATAAGGAAAACTCAGAAAATGA
TTATTAAGAAGAGAGAACCATTAAATTTTAGCGTCCCAGATGGTGCACAGGTTTCTCCAGTAGATTAGCTGCTACACAAG
ATATGCCTCTTATTCACCAATCTTCTGAATTAGGTGACATGTATACCTGGCAAGAAAATAGCAATGCATGGGAAGAAGAA
GAAGAAGATGCAGCCTGGCAAGCAGAGAATAGCAGACAAAGAGAGCAGCAGAGAGGCAGAGGGAGAAAATGGAAAAGGAA
GCACAGAGGCTC

Alignment

ORF - retro_itri_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.39 %
• Parental protein coverage: 90.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AITQFRL-FKVCTCLA-TVFSFLKRLICRSGRGRKLSGDQITLPTTVDYSSVPKQTDVEEW-TSWDEDAP
          AITQFRL.FKVCTCLA.TVFS.LKRLICRSG.G.KLSGDQITLPTT.DY.SVPKQTDVEE...SWDEDAP
Retrocopy AITQFRL>FKVCTCLA<TVFSVLKRLICRSGKGSKLSGDQITLPTTGDYPSVPKQTDVEEG<ASWDEDAP

Parental  T-SVKIEGGNGNVATQQNALEQMEPDYFKDMTPTIRKTQKIIIKKREPLNFGVPDGS-TGFSSRLAATQD
          T.S.K..GGNG.VA.QQNALEQMEPDYFK.MTPTIRKTQK.IIKKREPLNF.VPDG..TGFSSRLAATQD
Retrocopy T<SAKAKGGNGKVAAQQNALEQMEPDYFKGMTPTIRKTQKMIIKKREPLNFSVPDGA<TGFSSRLAATQD

Parental  MPFIHQSSELGDLDTWQENTNAW-EEEEDAAWQAEEVLRQ-QKIADREKRAAEQQRKKM
          MP.IHQSSELGD..TWQEN.NAW.EEEEDAAWQAE...RQ....A.R.....E......
Retrocopy MPLIHQSSELGDMYTWQENSNAWEEEEEDAAWQAEN-SRQ<KRAAERQREKMEKEAQRL

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_1119 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1119 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119 ,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,