RetrogeneDB ID: retro_itri_345

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393285.1:24354478..24354851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000026840
• Aliases: None
• Description: None

Sequence

>retro_itri_345
CCCGTACTTTCACTCCCTGAGCAAGGAATTAAAACGTTGGAGGAAGATGAAGAGGAACTTTTTAAAGATGCAAGCAAAGC
TACTTGGATTTGCTTCAGAGAATGATCTTCCAGGAGGAAGGAACCAGGCGCCCTCGAAGTTGAACATGAGAAAAGGACCA
TCTGCCTTCTCCTGAGGAGGGACAAGCCCCTGAAGATACACCCCAGCCACTGTATCCCACCGAGGCTGGGCTGAAGGCAA
ACCCGGCAACCACCATGCCTGGGTTTGGAACCCCTGTGCTCACTTTGGTGACGAGGACCCCAAGCAGGGACTGCTGTCAA
TCGGCTTCCTAAACGCTGGTCAGGCACAACATTCAAAACAGTCTGAAGAATGC

Alignment

ORF - retro_itri_345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.72 %
• Parental protein coverage: 64.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PIVSLPEQEIKTLEEDEEELFK-MRAKLFRFASENDLP-EWKERGTGDVKLLKHKEKGTIRLLMRRDKTL
          P..SLPEQ.IKTLEEDEEELFK.M.AKL..FASENDLP...KE.G...V....H.......LL.RRDK.L
Retrocopy PVLSLPEQGIKTLEEDEEELFK>MQAKLLGFASENDLP<RRKEPGALEV---EHEKRTICLLL-RRDKPL

Parental  KICANHYITPTM-ELKPN-AGSDRAWVWNTHADFADEYPKPELLAIRFLNAENAQKFKTKFEEC
          KI...H.I.P....LK.N..G...AWVWN..A.F.DE.PK..LL.I.FLNA..AQ..K...EEC
Retrocopy KIHPSHCIPPRL<GLKAN<PGNHHAWVWNPCAHFGDEDPKQGLLSIGFLNAGQAQHSK-QSEEC

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_345 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_345 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 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010749	1 retrocopy	retro_cjac_2619,
Cavia porcellus	ENSCPOG00000002962	1 retrocopy	retro_cpor_1249,
Dipodomys ordii	ENSDORG00000011317	2 retrocopies	retro_dord_241, retro_dord_602,
Echinops telfairi	ENSETEG00000015996	2 retrocopies	retro_etel_1018, retro_etel_1518,
Homo sapiens	ENSG00000099901	2 retrocopies	retro_hsap_1727, retro_hsap_4797,
Gorilla gorilla	ENSGGOG00000000784	1 retrocopy	retro_ggor_170,
Macropus eugenii	ENSMEUG00000016620	8 retrocopies	retro_meug_1064, retro_meug_1553, retro_meug_1670, retro_meug_1795, retro_meug_272, retro_meug_422, retro_meug_657, retro_meug_753,
Myotis lucifugus	ENSMLUG00000017535	1 retrocopy	retro_mluc_1429,
Macaca mulatta	ENSMMUG00000020100	1 retrocopy	retro_mmul_1215,
Monodelphis domestica	ENSMODG00000010312	5 retrocopies	retro_mdom_1290, retro_mdom_1397, retro_mdom_1406, retro_mdom_1996, retro_mdom_288,
Mus musculus	ENSMUSG00000005732	1 retrocopy	retro_mmus_3632,
Nomascus leucogenys	ENSNLEG00000005684	2 retrocopies	retro_nleu_2991, retro_nleu_934,
Otolemur garnettii	ENSOGAG00000034333	2 retrocopies	retro_ogar_1428, retro_ogar_2735,
Pongo abelii	ENSPPYG00000011593	4 retrocopies	retro_pabe_1438, retro_pabe_1470, retro_pabe_3731, retro_pabe_943,
Rattus norvegicus	ENSRNOG00000001884	4 retrocopies	retro_rnor_1817, retro_rnor_811, retro_rnor_884, retro_rnor_907,
Sarcophilus harrisii	ENSSHAG00000006873	1 retrocopy	retro_shar_9,
Ictidomys tridecemlineatus	ENSSTOG00000026840	2 retrocopies	retro_itri_1579, retro_itri_345 ,
Tarsius syrichta	ENSTSYG00000013573	1 retrocopy	retro_tsyr_320,
Tursiops truncatus	ENSTTRG00000008142	2 retrocopies	retro_ttru_456, retro_ttru_890,