RetrogeneDB ID: retro_itri_1175

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393394.1:417432..417816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSSTOG00000005084
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_itri_1175
TACAACAGGTATCTGGCTGAGTTTGCCATACGAAATGACAGGAAGGTGGCTGCAGAGAACAGTGTAGTGGCTTATAAAGC
TGCTAGTGATATTGCAATGACAGAACTTCAACCAACACACCCCATTCATTTAGATCTTGCTCTCAATTTTTCTGTATTCT
ACTATGAAATTCTTAATTACCCTGACCTTGACTGAAAGTTGGCAAAAGCAGATTTTGGTGATGCAGTTGCAGAACTGGAT
ACACTGAGTGAAGAAAGCTATAAGGACTCTACACTTATCATGCAATTGTTGCGTAATAACCTGACACTATAGACTTCATA
CATGCAGGGTGATGGTGAAGACCAGCATAAAAAAGCGCCGCAGGATATGGAAGGTGAAAATCAG

Alignment

ORF - retro_itri_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.47 %
• Parental protein coverage: 54.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKA
          Y.RYLAEFA..NDRK.AAENS.VAYKAASDIAMTEL.PTHPI.L.LALNFSVFYYEILN.PD....LAKA
Retrocopy YNRYLAEFAIRNDRKVAAENSVVAYKAASDIAMTELQPTHPIHLDLALNFSVFYYEILNYPDLD*KLAKA

Parental  AFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ
          .F.DA.AELDTLSEESYKDSTLIMQLLR.NLTL.TS.MQGDGE.Q.K.A.QD.E.ENQ
Retrocopy DFGDAVAELDTLSEESYKDSTLIMQLLRNNLTL*TSYMQGDGEDQHKKAPQDMEGENQ

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_1175 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1175 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 16 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000003733	1 retrocopy	retro_itri_1214,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175 ,
Ictidomys tridecemlineatus	ENSSTOG00000023864	3 retrocopies	retro_itri_162, retro_itri_483, retro_itri_887,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,