RetrogeneDB ID: retro_itri_1160

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393390.1:1795561..1796176(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSSTOG00000013200
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_itri_1160
GGTCTCGGTCCAGTTCCACCTCCAGCTCAGGATCCAGGACCAGCACAGGCTCAGGCAGTGGCTCCAGCTCTTCCTCTGCA
TCTCAGAAGCTCCAGGACCTCCTGCAGCTGCAGCTCCAGCGGTTCCCCCATCTCCCAGCCCTTCTCGGTGACAAAAGGCC
GCGCTCCGGCTCCAAATCCACGCCACCTAAAGAGAAGGAAAGGGAAGGAAAAGGCGGAGCCCTTCCCCTAAACCTACCAA
AGTGCATATTGGAAGGCTCACCAGGAATGTGACCAAGGATCACATCACAGAGATGCTTTCTACCTATGGAAAAACTAAAA
TGACTGGCACGCCTGTGGGCAGGATGCATCCTCATCCATCCAGAGGCTGTGCACAGCTGGAGTTGGAGAGTCTAGATGAA
GTGAGAAGGCGCTGAAGCGCGTGGATGGAAGACAAGTTGATGGCCAGGAGATCGCTGCTACTGCTGTGCTGGCCCCCTGG
CCTAGGCCACCCCCCAGGCGATTCAGCCCTCCCAGGAGAATGCTGCCGCCACCTCCCATGTGGCCCAGGTCACCCCCACG
GAAGAGGAGGAGGTCACGCTCCCCAAGACGCAGGTCCCCCATGCGTGGGCGGTCC

Alignment

ORF - retro_itri_1160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLGPVPPPAQDPVPAQAQAV-WSTKSRTLHKLGLHWTTVLHLQPKSSTLWLDRNCLLSFRSKPPKRDEKE
          GLGPVPPPAQDP.PAQAQAV..S..S....KL.......L...P....L..D........S.PPK..E.E
Retrocopy GLGPVPPPAQDPGPAQAQAV<GSSSSSASQKLQDLLQLQLQRFPHLPALLGDKRPRSGSKSTPPKEKERE

Parental  RKRRS-PLNLPKCILEDSPGMKDHI--MEIFSTYGKIK-MIDMPVERMHPHLSKGYAYVEFENPDE-AEK
          .K....PLNLPKCILE.SPGM...I.....F....K.K.M...PV.RMHPH.S.G.A..E.E..DE..EK
Retrocopy GKGGALPLNLPKCILEGSPGM*PRITSQRCFLPMEKLK<MTGTPVGRMHPHPSRGCAQLELESLDE<SEK

Parental  ALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPMRRRS
          ALK..DG.Q.DGQEI.ATAVLAPWPRPPPRRFSPPRRMLPPPPMW.RSPPR.RRRSRSPRRRSPMR.RS
Retrocopy ALKRVDGRQVDGQEIAATAVLAPWPRPPPRRFSPPRRMLPPPPMWPRSPPRKRRRSRSPRRRSPMRGRS

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_1160 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1160 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 25 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017861	1 retrocopy	retro_amel_194,
Bos taurus	ENSBTAG00000009969	7 retrocopies	retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris	ENSCAFG00000019397	1 retrocopy	retro_cfam_449,
Choloepus hoffmanni	ENSCHOG00000004866	4 retrocopies	retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Callithrix jacchus	ENSCJAG00000014969	2 retrocopies	retro_cjac_2127, retro_cjac_3377,
Cavia porcellus	ENSCPOG00000002066	2 retrocopies	retro_cpor_363, retro_cpor_953,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Felis catus	ENSFCAG00000007690	1 retrocopy	retro_fcat_248,
Homo sapiens	ENSG00000205937	1 retrocopy	retro_hsap_2911,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta	ENSMMUG00000019238	1 retrocopy	retro_mmul_794,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Oryctolagus cuniculus	ENSOCUG00000004387	2 retrocopies	retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Pan troglodytes	ENSPTRG00000031310	1 retrocopy	retro_ptro_1967,
Pteropus vampyrus	ENSPVAG00000005105	1 retrocopy	retro_pvam_296,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160 ,
Tupaia belangeri	ENSTBEG00000009098	8 retrocopies	retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta	ENSTSYG00000001629	1 retrocopy	retro_tsyr_957,
Tursiops truncatus	ENSTTRG00000008220	7 retrocopies	retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,