RetrogeneDB ID: retro_itri_1783

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393767.1:411971..412831(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024628
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C9orf78
• Ensembl ID: ENSSTOG00000020630
• Aliases: None
• Description: chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]

Sequence

>retro_itri_1783
ATGTCAGTCACCGGGAAGATGTTTCCTCTGTGATGGGCCAACTCTGAGTCGGAGGAAGATAATGAGGATTTGGAGGAGGT
TCGGCTAAAACTGGAAGAGGCCCGAGAGGTGCAGAACTTGAGAAAGAGGCCCAACTTGGTGAGTGCTGCTGCCCTGCTGG
TGGGAGAGAAGGTAAAGAAGAGACCACACGAGTGGATGATCCCTTTCAGATGAAGACAGGTGGTATGGTGGACACGAAGA
AATTGAAGGAAAGGGGGAAAGATTAGTGAAGAAGAGGACGTTCATCTGGGTACATCGTTTTCTGCAGAAACCAATTGGAG
GGATGAAGATGCAGACATGATGAAGTACATTGAGACAGAGCTAAAGAAGAAGAAAAGGATTGTGGAACATGAGGAACTGA
AAATCAAGCCAAAGAACGCAGAGGGCTGTCTATATGAACTTCCTGAAAACACCCGCATGTCCTCTGCAAAGAAGACTGAG
GAGATGCTTTCCAACCAGATGCTGAGTGGCATCCCCGAGGTGGACCTGGGCATCGAGGCAAAAATTTAAAAAATATCATT
TGCACGGAGGATGCCAAGGCTCGCCTGCTGGCAGAGCAGCAGAACAAGAAGAAAGACAGTGAGACATCCTTCGTGCCCAC
GAACAAAGCTGTGAATTACGTGCAATACAACCGATTTTATCATGAGGAGCTCAATGCTCCCATCTGGAGAAACAAAGAGC
CCAAAGCTCGGCCCTTGCGAGTGGGTGACACTGAGAAGCCAGAGCCTGAGCCGTCTGCTCCTAACCGCAAGCATCCTGCT
AATGAAAAGGCCACTGATGACTACCACTATGATAAGTTCAAGAAGATGAACAGGCGGTAC

Alignment

ORF - retro_itri_1783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPVTGKMFRRRRADSESEEDEQDSEEVRLKLEETREVQNLRKRPNGVSAAALLVGEKV-QEETTLVDDPF
          M.VTGKMF....A.SESEED..D.EEVRLKLEE.REVQNLRKRPN.VSAAALLVGEKV..EETT.VDDPF
Retrocopy MSVTGKMFPL*WANSESEEDNEDLEEVRLKLEEAREVQNLRKRPNLVSAAALLVGEKV<KEETTRVDDPF

Parental  QMKTGGMVDMKKLKERGKD-KISEEEDLHLGTSFSAETNRRDEDADMMKYIESELKKRKGIVEHEEQKIK
          QMKTGGMVD.KKLKERGKD....E...L....S........D.D.......E...KKR..IVEHEE.KIK
Retrocopy QMKTGGMVDTKKLKERGKD>SEEEDVHLGTSFSAETNWRDEDADMMKYIETELKKKKR--IVEHEELKIK

Parental  PKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKNI-ISTEDAKARLLAEQQNKK-K
          PKNAE.CLYELPEN.R.SSAKKTEEMLSNQMLSGIPEVDLGI.AKI..I.I.........L...Q..K.K
Retrocopy PKNAEGCLYELPENTRMSSAKKTEEMLSNQMLSGIPEVDLGIEAKI*KI<IICTEDAKARLLAEQQNKKK

Parental  DSETSFVPTNMAVNYVQHNRFYHEELNAPIRRNKEEPKARPLRVGDTEKPEPERSPPNRKRPANEKATDD
          DSETSFVPTN.AVNYVQ.NRFYHEELNAPI.RNK.EPKARPLRVGDTEKPEPE.S.PNRK.PANEKATDD
Retrocopy DSETSFVPTNKAVNYVQYNRFYHEELNAPIWRNK-EPKARPLRVGDTEKPEPEPSAPNRKHPANEKATDD

Parental  YHYEKFKKMNRRY
          YHY.KFKKMNRRY
Retrocopy YHYDKFKKMNRRY

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_1783 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1783 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783 ,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,