RetrogeneDB ID: retro_itri_1900

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH397736.1:3250..3548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000010902
• Aliases: None
• Description: None

Sequence

>retro_itri_1900
ATGGCTCTCACAAAGAAAGGTAGTAAGAGCTGTTCTCCCATCATTGAGGTGGTGACCACAGAATTGCACAATTCCCATCC
ACAAGTGCAGCCATGGAGAGGGCCTCGAAAAACATTCTCCCCGGGCACTCAAAGAGATCTGGAAATTCGCCACGAAAGAG
ATGGGAGCTCCAGATGTGCTGGGTTGACACCAGACTCCGCAGAGCTCTCTGAGCAAAGGCATATGGACTGTCCCCTACCA
TACCCACGTGGGGTTGTCCAGAAAGACTAATGAGGATGAACGGTCACCAAATAAGCTC

Alignment

ORF - retro_itri_1900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 81.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPAKKGGEKKKGRSAINEVVTREY-TINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVR-IDTRL
          MA..KKG....K..S.I.EVVT.E..TI.IHK..HG.G..K..PRALKEI.KFA.KEMG.PDV...DTRL
Retrocopy MALTKKGS---KSCSPIIEVVTTEL>TIPIHKCSHGEGLEKHSPRALKEIWKFATKEMGAPDVL>VDTRL

Parental  NKAVWA-KGIRNVPYRIRVRLSRKRNEDEDSPNKL
          ..A..A.KGI..VPY...V.LSRK.NEDE.SPNKL
Retrocopy RRAL*A<KGIWTVPYHTHVGLSRKTNEDERSPNKL

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_1900 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1900 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 10 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007914	1 retrocopy	retro_acar_168,
Bos taurus	ENSBTAG00000019701	9 retrocopies	retro_btau_1043, retro_btau_1100, retro_btau_1553, retro_btau_160, retro_btau_1777, retro_btau_1783, retro_btau_409, retro_btau_524, retro_btau_867,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Monodelphis domestica	ENSMODG00000001704	5 retrocopies	retro_mdom_1052, retro_mdom_1464, retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Oryctolagus cuniculus	ENSOCUG00000002392	9 retrocopies	retro_ocun_1070, retro_ocun_1074, retro_ocun_1161, retro_ocun_117, retro_ocun_1366, retro_ocun_206, retro_ocun_64, retro_ocun_941, retro_ocun_99,
Sarcophilus harrisii	ENSSHAG00000011706	3 retrocopies	retro_shar_190, retro_shar_285, retro_shar_721,
Ictidomys tridecemlineatus	ENSSTOG00000010902	15 retrocopies	retro_itri_1068, retro_itri_1074, retro_itri_1077, retro_itri_1140, retro_itri_1142, retro_itri_1223, retro_itri_1467, retro_itri_1570, retro_itri_1634, retro_itri_1791, retro_itri_1900 , retro_itri_298, retro_itri_450, retro_itri_680, retro_itri_76,
Tarsius syrichta	ENSTSYG00000005427	33 retrocopies	retro_tsyr_1102, retro_tsyr_117, retro_tsyr_1211, retro_tsyr_1535, retro_tsyr_1610, retro_tsyr_1692, retro_tsyr_1861, retro_tsyr_1912, retro_tsyr_1947, retro_tsyr_2001, retro_tsyr_2026, retro_tsyr_2030, retro_tsyr_2079, retro_tsyr_2089, retro_tsyr_2092, retro_tsyr_2100, retro_tsyr_2105, retro_tsyr_2162, retro_tsyr_239, retro_tsyr_294, retro_tsyr_485, retro_tsyr_551, retro_tsyr_596, retro_tsyr_617, retro_tsyr_635, retro_tsyr_666, retro_tsyr_712, retro_tsyr_754, retro_tsyr_766, retro_tsyr_780, retro_tsyr_785, retro_tsyr_813, retro_tsyr_909,