RetrogeneDB ID: retro_itri_737

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393315.1:9803514..9804588(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000012843
• Aliases: None
• Description: None

Sequence

>retro_itri_737
TTTGAGGGTGCTAAAGCAGGTATTCAGATCTATCCCAAGAACTATACAGATAATGAATTGGAGAAGATCACAAGAAGGTT
TACCATGGAGTGTGCAGAAAAAGGTTTTACTGGTCCTGGCATTGATGTGCCTGTCCCAGACATGAGCACAGGCTATCGGA
AGATGTCCTCTATCACTGTCACCTATGCCAGCACCATAGGGCACTATAATATTAATGCACATGCCTGTGTTACTGGTAAA
TTCATCAGTCAAGAATGCATCCACAGAGTCATCTCTGCTACTAGCCTGAATGTTTTCTATGGGATTGAAAACTTCATTAA
TGAAGCTTCTTACAGGAGCATTTTAGGAATAACACAAGGATTTGGAGATAAAACATTTGTGGTTCAGGGACTTGGTAACA
TGGGCCAGCACTTTATGAGGTATTTACATTGTTTTGGTGCTAAATGTATTGGTGTTGGTGAATCTGATGGGATATACGGA
ATCCAGATGTTATTGACCCAAAGGAACTAGAAAATTTCAGATTGTCACATGGATCAATTCTGGGCTTCCCCAAGGCAAAG
GTATATGAAGAAAGTATCTTGGAGGCTGACTGTGAAATACTGATCCCTGCTGCATGTGAGAAGCAGTTGACCAAATCCCA
TGCACCCAGAGTCAAAGCCAAGATTATGGCTGAAGGTGCAAAAGGACCAACTACTCCAGAAGCTGATAAGATTCTCCTGG
AGAGGAACATCATGGTTATTCCAGATCTCTACTTAAATGCTGGTGGAGTGACAGTATCTTACTTTGAGAGGCTGAAGAAT
CTGAATCATGTCAGCTATGGCTGATTAACCTTCAAATATGAACGGGATTCTAACTACCCCTTGTTCATGTCTGTTCAAGA
GTGTTTTGAATGAAAATTTGGAAAGCATGGTGGAATAATTCCGTTGTACTCACCACAGTGTTCCAGGATAGGATAGTGAG
TGCATGATAGAAAGACCCTGTGCATTCTGGCTTAGCCTATACCTGGAGCATTCAGCCATGCAAATTGTGCGTTGGACCAT
GAAGTATAACCTGGGCTTGGACCTGAGAACAGCT

Alignment

ORF - retro_itri_737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 87.56 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYD
          F.GAKAG..I.PKNYTDNELEKITRRFTME.A.KGF.GPGIDVP.PDMSTG.R.MS.I..TYASTIGHY.
Retrocopy FEGAKAGIQIYPKNYTDNELEKITRRFTMECAEKGFTGPGIDVPVPDMSTGYRKMSSITVTYASTIGHYN

Parental  INAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMR
          INAHACVTGK.ISQ..IH..ISAT...VF.GIENFINEASY.SILG.T.GFGDKTFVVQG.GN.G.H.MR
Retrocopy INAHACVTGKFISQECIHRVISATSLNVFYGIENFINEASYRSILGITQGFGDKTFVVQGLGNMGQHFMR

Parental  YLHRFGAKCVGVGESDG-SIWNPDGIDPKELEDFKLQHGSILGFPKAKVYEGSILEADCDILIPAASEKQ
          YLH.FGAKC.GVGESDG..I.NPD.IDPKELE.F.L.HGSILGFPKAKVYE.SILEADC.ILIPAA.EKQ
Retrocopy YLHCFGAKCIGVGESDG<DIRNPDVIDPKELENFRLSHGSILGFPKAKVYEESILEADCEILIPAACEKQ

Parental  LTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFK
          LTKS.APRVKAKI.AEGA.GPTTPEADKI.LERNIMVIPDLYLNAGGVTVSYFE.LKNLNHVSYG.LTFK
Retrocopy LTKSHAPRVKAKIMAEGAKGPTTPEADKILLERNIMVIPDLYLNAGGVTVSYFERLKNLNHVSYG*LTFK

Parental  YERDSNYHLLMSVQESLERKFGKHGGTIP-IVPTAEFQDRISGASEKDIVHSGLAYT-MERSARQIMRTA
          YERDSNY.L.MSVQE..E.KFGKHGG.IP..V.T..FQDRI..A..KD.VHSGLAYT..E.SA.QI.R..
Retrocopy YERDSNYPLFMSVQECFE*KFGKHGGIIP<VVLTTVFQDRIVSA**KDPVHSGLAYT<LEHSAMQIVRWT

Parental  MKYNLGLDLRTA
          MKYNLGLDLRTA
Retrocopy MKYNLGLDLRTA

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_737 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_737 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737 ,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,