RetrogeneDB ID: retro_itri_1030

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393360.1:1488894..1489497(+)
• Located in intron of: ENSSTOG00000006735

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000008658
• Aliases: None
• Description: None

Sequence

>retro_itri_1030
CAGGTACAATGCTTCAGTACATCTGTGGTCAGACCATTTACCAAACTTGTGAAGGCCACCTGTTCAGATACATAGCATTG
AAGGTCACTATGCCACTGCTTTTATTCTGCTGCATCTAAACAGAATTAACTGGAACAAGTAGAAAAGCAGTTGTTGAGAG
TAGCACAACTCCTGAAGGAACCCAAAGTGGCTGCTTCTATTCTAAATCCTTATAGTAAGCATTCCATCAAAATGAAAAGT
CTAAATGACATGACAGCAAAAAAGTTTTTTTTCGCATTATATCTAACCTGTAAACTTGCTTGCTGAAATGGTCTCCTAAA
CAATACCCTTGCCATCATTTCTGCCTTTTCTACAATTATGAGTGTGCACCATGGAGAAGTACCTTCTACAGTGACCACCA
TATCTCCTTTAGTGGAAGCTAATCCTTCTGAGTTAAAGACAGTCCTGAAGAGCTTCCTAAGTCAAGGCCAAGTATTGAAA
TTGGAGGTTAAGATTGATCCAGCATTTATGAGTGGGATAATTGTCCATATTGGAGATAAATATGTTGATATGTCTGTAAA
AACCAAGATTCAGGAGCTAATCTGCGCTTTGTGGGAGAGTATC

Alignment

ORF - retro_itri_1030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KVRCFSTSMVRPFTKLV-RPPVQVYGVEGRYATAL-YSAASKQNKLEQVEKELLRVAQILKEPKTAASIL
          .V.CFSTS.VRPFTKLV.RPPVQ....EG.YATA..YSAASKQN.LEQVEK.LLRVAQ.LKEPK.AASIL
Retrocopy QVQCFSTSVVRPFTKLV>RPPVQIHSIEGHYATAF<YSAASKQN*LEQVEKQLLRVAQLLKEPKVAASIL

Parental  NPHIKRSIKMKSLNDITAKERFSP-ITSNL-INLLAE-NGRLGSAHGIISAFSTIMSVHRGEVPCTVTTA
          NP..K.SIKMKSLND.TAK......I.SNL..NLLAE.NG.L.....IISAFSTIMSVH.GEVP.TVTT.
Retrocopy NPYSKHSIKMKSLNDMTAKKXXXA<IISNL<VNLLAE<NGLLNNTLAIISAFSTIMSVHHGEVPSTVTTI

Parental  SPLPEAVLSELKTVLKSFLSQGQVLKLEVKTDPAIMGGMIVRIGEKYVDMSAKTKIQKLTRAMRESI
          SPL.EA..SELKTVLKSFLSQGQVLKLEVK.DPA.M.G.IV.IG.KYVDMS.KTKIQ.L..A..ESI
Retrocopy SPLVEANPSELKTVLKSFLSQGQVLKLEVKIDPAFMSGIIVHIGDKYVDMSVKTKIQELICALWESI

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_1030 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1030 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 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014708	1 retrocopy	retro_amel_1914,
Canis familiaris	ENSCAFG00000009541	3 retrocopies	retro_cfam_1277, retro_cfam_2198, retro_cfam_235,
Choloepus hoffmanni	ENSCHOG00000011242	1 retrocopy	retro_chof_638,
Callithrix jacchus	ENSCJAG00000002873	1 retrocopy	retro_cjac_1567,
Equus caballus	ENSECAG00000009059	1 retrocopy	retro_ecab_633,
Echinops telfairi	ENSETEG00000000807	5 retrocopies	retro_etel_1412, retro_etel_1906, retro_etel_507, retro_etel_839, retro_etel_841,
Felis catus	ENSFCAG00000028656	1 retrocopy	retro_fcat_1511,
Homo sapiens	ENSG00000241837	1 retrocopy	retro_hsap_2377,
Gorilla gorilla	ENSGGOG00000012611	1 retrocopy	retro_ggor_1803,
Macropus eugenii	ENSMEUG00000006613	4 retrocopies	retro_meug_122, retro_meug_1552, retro_meug_381, retro_meug_805,
Myotis lucifugus	ENSMLUG00000008224	3 retrocopies	retro_mluc_1833, retro_mluc_826, retro_mluc_856,
Macaca mulatta	ENSMMUG00000015504	1 retrocopy	retro_mmul_253,
Monodelphis domestica	ENSMODG00000021057	2 retrocopies	retro_mdom_280, retro_mdom_95,
Mustela putorius furo	ENSMPUG00000001319	5 retrocopies	retro_mputfur_1593, retro_mputfur_1628, retro_mputfur_1639, retro_mputfur_581, retro_mputfur_918,
Mus musculus	ENSMUSG00000022956	2 retrocopies	retro_mmus_2196, retro_mmus_955,
Otolemur garnettii	ENSOGAG00000015850	4 retrocopies	retro_ogar_3518, retro_ogar_418, retro_ogar_559, retro_ogar_944,
Pongo abelii	ENSPPYG00000011384	1 retrocopy	retro_pabe_2247,
Pan troglodytes	ENSPTRG00000013876	1 retrocopy	retro_ptro_1739,
Rattus norvegicus	ENSRNOG00000001991	1 retrocopy	retro_rnor_2210,
Sarcophilus harrisii	ENSSHAG00000000409	3 retrocopies	retro_shar_369, retro_shar_389, retro_shar_668,
Sus scrofa	ENSSSCG00000012042	2 retrocopies	retro_sscr_226, retro_sscr_566,
Ictidomys tridecemlineatus	ENSSTOG00000008658	3 retrocopies	retro_itri_1030 , retro_itri_565, retro_itri_794,