RetrogeneDB ID: retro_itri_643

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:3554472..3554801(-)
• Located in intron of: ENSSTOG00000000455

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS26
• Ensembl ID: ENSSTOG00000010559
• Aliases: None
• Description: ribosomal protein S26 [Source:HGNC Symbol;Acc:10414]

Sequence

>retro_itri_643
ACCAAAAAAAGAAGAAATAATGGTCAGGCCAAAAAAGCCACAGCCATGTGCAGCCTATTTGTTGCTCAAACTGTGCCAGG
TGCATGCCAAGGACAGGCCATTAAGAAGTTCACCATTTGAAACACCTCAGCCATCAGGGACATTTCTAAAGCAAGTATTT
TAATGCTTATGTGTTTCCCAAGCTCCATGTAAAGGTGCATTACTGTGTGAGTTATGCCATTCACAGCAAGGTGGTCAGGA
ATCGATCTCATGAAGCCTGGAAGGACTGAATACTCCCACTCCATTTTAGACCTGCTAGTGCCACCCCATAACCTCCACCA
AAGCCCATG

Alignment

ORF - retro_itri_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TKKRRNNGRAKKG-RGHVQPIRCTNCARCVP-KDK-AIKKFVIRNIVEAAAVRDISEASV-FDAYVLPKL
          TKKRRNNG.AKK....HVQPI.C.NCARC.P.KD..AIKKF.I.N.....A.RDIS.AS..F.AYV.PKL
Retrocopy TKKRRNNGQAKKA<HSHVQPICCSNCARCMP<KDR<AIKKFTI*N---TSAIRDISKASI<FNAYVFPKL

Parental  YVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM
          .VK.HYCVS.AIHSKVVRNRS.EA.KD...P..FRPA.A.P.PPPKPM
Retrocopy HVKVHYCVSYAIHSKVVRNRSHEAWKD*ILPLHFRPASATP*PPPKPM

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_643 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_643 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 126 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038896	3 retrocopies	retro_btau_191, retro_btau_25, retro_btau_724,
Cavia porcellus	ENSCPOG00000023630	6 retrocopies	retro_cpor_115, retro_cpor_1231, retro_cpor_134, retro_cpor_173, retro_cpor_48, retro_cpor_992,
Dipodomys ordii	ENSDORG00000001151	2 retrocopies	retro_dord_239, retro_dord_279,
Echinops telfairi	ENSETEG00000004510	35 retrocopies	retro_etel_1072, retro_etel_1145, retro_etel_1149, retro_etel_1175, retro_etel_1321, retro_etel_1357, retro_etel_1407, retro_etel_1423, retro_etel_1469, retro_etel_1498, retro_etel_155, retro_etel_162, retro_etel_1647, retro_etel_1691, retro_etel_1703, retro_etel_1734, retro_etel_1801, retro_etel_181, retro_etel_1859, retro_etel_1913, retro_etel_1963, retro_etel_2006, retro_etel_2043, retro_etel_2138, retro_etel_2146, retro_etel_2175, retro_etel_269, retro_etel_354, retro_etel_38, retro_etel_424, retro_etel_462, retro_etel_741, retro_etel_77, retro_etel_894, retro_etel_898,
Gorilla gorilla	ENSGGOG00000011566	6 retrocopies	retro_ggor_106, retro_ggor_121, retro_ggor_19, retro_ggor_55, retro_ggor_56, retro_ggor_63,
Loxodonta africana	ENSLAFG00000013329	8 retrocopies	retro_lafr_180, retro_lafr_240, retro_lafr_40, retro_lafr_464, retro_lafr_513, retro_lafr_768, retro_lafr_835, retro_lafr_962,
Myotis lucifugus	ENSMLUG00000029968	10 retrocopies	retro_mluc_1153, retro_mluc_149, retro_mluc_1925, retro_mluc_2065, retro_mluc_2163, retro_mluc_2462, retro_mluc_266, retro_mluc_309, retro_mluc_332, retro_mluc_477,
Macaca mulatta	ENSMMUG00000017042	7 retrocopies	retro_mmul_1009, retro_mmul_1017, retro_mmul_1676, retro_mmul_1944, retro_mmul_2092, retro_mmul_294, retro_mmul_646,
Mus musculus	ENSMUSG00000025362	1 retrocopy	retro_mmus_115,
Pongo abelii	ENSPPYG00000004642	16 retrocopies	retro_pabe_1234, retro_pabe_1372, retro_pabe_140, retro_pabe_1405, retro_pabe_1431, retro_pabe_155, retro_pabe_1613, retro_pabe_237, retro_pabe_25, retro_pabe_2835, retro_pabe_3068, retro_pabe_3399, retro_pabe_3432, retro_pabe_809, retro_pabe_903, retro_pabe_924,
Pan troglodytes	ENSPTRG00000005075	1 retrocopy	retro_ptro_74,
Rattus norvegicus	ENSRNOG00000005517	1 retrocopy	retro_rnor_196,
Sus scrofa	ENSSSCG00000000374	2 retrocopies	retro_sscr_406, retro_sscr_650,
Ictidomys tridecemlineatus	ENSSTOG00000010559	12 retrocopies	retro_itri_1300, retro_itri_1446, retro_itri_1477, retro_itri_1488, retro_itri_289, retro_itri_418, retro_itri_469, retro_itri_470, retro_itri_643 , retro_itri_652, retro_itri_729, retro_itri_871,
Tursiops truncatus	ENSTTRG00000015012	16 retrocopies	retro_ttru_1169, retro_ttru_1300, retro_ttru_131, retro_ttru_1319, retro_ttru_1329, retro_ttru_1412, retro_ttru_1514, retro_ttru_1635, retro_ttru_17, retro_ttru_1734, retro_ttru_1795, retro_ttru_1897, retro_ttru_428, retro_ttru_47, retro_ttru_651, retro_ttru_893,