RetrogeneDB ID: retro_itri_1858

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394194.1:69810..70521(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSSTOG00000024252
• Aliases: None
• Description: tropomyosin 4 [Source:HGNC Symbol;Acc:12013]

Sequence

>retro_itri_1858
CGCAAGATCCAGGCCCTGCAGCAGCAGGCGGTCGAGTTGGAGGACCGCGCTCAGAGCCTGCTGCGGGAGCTGGACTGCGA
GCGCGAGCAGCGCGAAAAAGCCAAAGATGATGTGGCAGCTCTCAACAGACGCATCCAGTTGGTGGAGGAGGAGCTGGACA
GGGCCCAGGAACGGCTGGCCACTGCCCTGCAGAAGCTGGAGGAGGCAGAAAAGGCTGCGGATGAGAGCGACAGGGGAATG
AAGGTGATACAAAACCGCACCATGAAGGACGAGGAGAAGATGGAGATTCAGGAGATGCAGCTCAAAGAGGCCAAGCACAT
CGCCGAGGAGGCCGACCGCAAGTACGAGGAGGTGGCTCGGAAGCTGGTCATCCTGGAGGGCGAGCTGGAGAGGGCAGAGG
AGCGTGCGGAGGTGTCTGAACTAAAATGTGAGGACCTGGAAGAAGAACTCAAGAATGTCACTAACAATCTGAAATCGCTG
GAGGCTGCATCTGAAAAGTACTCTGAAAAGGAGGATAAATATGAATTAGAAATTAAACTTCTGTCAGACAAGCTGAAGGA
GGCCGAGACTCGCGCTGAATTTGAAGAGAGAACAGTGGCCAAACTGGAAAAGACGATCGACGACCTGGAAGAAAAACTTG
CCCAGGCCAAAGAAGAGAACATGGGCCTACATCAGACACTGGATCAGACACTAAATGAACTTAACTGTATA

Alignment

ORF - retro_itri_1858 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.12 %
• Parental protein coverage: 95.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKLKGTEDELDKYSEDLKDAQEKLELTEKKASDAEGDVAALNRRIQLVEEELDRAQERLATALQKLEEAE
          .K.....................L.........A..DVAALNRRIQLVEEELDRAQERLATALQKLEEAE
Retrocopy RKIQALQQQAVELEDRAQSLLRELDCEREQREKAKDDVAALNRRIQLVEEELDRAQERLATALQKLEEAE

Parental  KAADESERGMKVIENRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAEVSE
          KAADES.RGMKVI.NR.MKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAEVSE
Retrocopy KAADESDRGMKVIQNRTMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAEVSE

Parental  LKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTVAKLEKTIDDLE
          LKC.DLEEELKNVTNNLKSLEAASEKYSEKEDKYE.EIKLLSDKLKEAETRAEF.ERTVAKLEKTIDDLE
Retrocopy LKCEDLEEELKNVTNNLKSLEAASEKYSEKEDKYELEIKLLSDKLKEAETRAEFEERTVAKLEKTIDDLE

Parental  EKLAQAKEENVGLHQTLDQTLNELNCI
          EKLAQAKEEN.GLHQTLDQTLNELNCI
Retrocopy EKLAQAKEENMGLHQTLDQTLNELNCI

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_1858 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1858 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 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604, retro_btau_1758,
Canis familiaris	ENSCAFG00000015796	1 retrocopy	retro_cfam_2107,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Monodelphis domestica	ENSMODG00000014882	1 retrocopy	retro_mdom_1354,
Mus musculus	ENSMUSG00000031799	1 retrocopy	retro_mmus_1625,
Nomascus leucogenys	ENSNLEG00000005413	2 retrocopies	retro_nleu_1952, retro_nleu_469,
Pan troglodytes	ENSPTRG00000010637	10 retrocopies	retro_ptro_1002, retro_ptro_1109, retro_ptro_1341, retro_ptro_1342, retro_ptro_1750, retro_ptro_1768, retro_ptro_2648, retro_ptro_2694, retro_ptro_2830, retro_ptro_516,
Pteropus vampyrus	ENSPVAG00000009755	2 retrocopies	retro_pvam_186, retro_pvam_187,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858 ,
Tupaia belangeri	ENSTBEG00000012927	7 retrocopies	retro_tbel_1435, retro_tbel_2468, retro_tbel_3663, retro_tbel_3709, retro_tbel_3872, retro_tbel_4651, retro_tbel_482,
Tarsius syrichta	ENSTSYG00000010642	9 retrocopies	retro_tsyr_1377, retro_tsyr_1613, retro_tsyr_1642, retro_tsyr_1853, retro_tsyr_628, retro_tsyr_694, retro_tsyr_704, retro_tsyr_742, retro_tsyr_749,
Tursiops truncatus	ENSTTRG00000014542	2 retrocopies	retro_ttru_504, retro_ttru_839,