RetrogeneDB ID: retro_itri_1026

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393359.1:8043666..8043966(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM136A
• Ensembl ID: ENSSTOG00000008343
• Aliases: None
• Description: family with sequence similarity 136, member A [Source:HGNC Symbol;Acc:25911]

Sequence

>retro_itri_1026
AGGGTGCAGGAGGTGGTGGACTCCATGGTGAAAAGGGTGGAGAGGGGGAATATCTGGAAGATGCAGGGCCTCGTGTTCTG
GTTCAGCACTAGCTGCTGTGAGGATAACCAGGCTTCCATGCAACAGGTACACCCGTGCATTGAGCACTGCCATGTGCCTC
TGGCTTAAGCCCAGGCCTTGGTAACCAGTAAGTTGGAGAAGCTCCAGAACCACCTGGCCTGGTGTACCATGCATAAAGCC
AAAGATTCAATATGTGCTGGGAGTAAAGAGCTTCAGGGGAAGTGGAAGCTAGACAGTTGT

Alignment

ORF - retro_itri_1026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.76 %
• Parental protein coverage: 74.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVQEAVDSMVKSVERENIRKMQGLMFRCSASCCEDSQASMQQVHQCIERCHAPLAQAQALVTSELEKFQD
          RVQE.VDSMVK.VER.NI.KMQGL.F..S.SCCED.QASMQQVH.CIE.CH.PLA.AQALVTS.LEK.Q.
Retrocopy RVQEVVDSMVKRVERGNIWKMQGLVFWFSTSCCEDNQASMQQVHPCIEHCHVPLA*AQALVTSKLEKLQN

Parental  RLARCTMHCNDKAKDSIDAGNKELQVKRQLDSC
          .LA.CTMH...KAKDSI.AG.KELQ.K..LDSC
Retrocopy HLAWCTMH---KAKDSICAGSKELQGKWKLDSC

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_1026 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1026 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 18 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015992	1 retrocopy	retro_amel_1454,
Bos taurus	ENSBTAG00000008674	2 retrocopies	retro_btau_37, retro_btau_88,
Canis familiaris	ENSCAFG00000003353	2 retrocopies	retro_cfam_1042, retro_cfam_148,
Cavia porcellus	ENSCPOG00000009117	1 retrocopy	retro_cpor_221,
Dasypus novemcinctus	ENSDNOG00000019447	7 retrocopies	retro_dnov_2036, retro_dnov_2465, retro_dnov_2612, retro_dnov_324, retro_dnov_620, retro_dnov_873, retro_dnov_901,
Dipodomys ordii	ENSDORG00000006529	4 retrocopies	retro_dord_365, retro_dord_391, retro_dord_733, retro_dord_778,
Felis catus	ENSFCAG00000008119	1 retrocopy	retro_fcat_1459,
Gorilla gorilla	ENSGGOG00000023247	6 retrocopies	retro_ggor_1361, retro_ggor_1625, retro_ggor_2155, retro_ggor_2356, retro_ggor_53, retro_ggor_8,
Macropus eugenii	ENSMEUG00000015791	8 retrocopies	retro_meug_1126, retro_meug_1351, retro_meug_1545, retro_meug_167, retro_meug_2131, retro_meug_219, retro_meug_457, retro_meug_719,
Macaca mulatta	ENSMMUG00000007962	5 retrocopies	retro_mmul_1421, retro_mmul_1772, retro_mmul_220, retro_mmul_327, retro_mmul_656,
Monodelphis domestica	ENSMODG00000011533	1 retrocopy	retro_mdom_65,
Mus musculus	ENSMUSG00000057497	2 retrocopies	retro_mmus_240, retro_mmus_3101,
Otolemur garnettii	ENSOGAG00000028265	4 retrocopies	retro_ogar_1788, retro_ogar_2273, retro_ogar_379, retro_ogar_684,
Rattus norvegicus	ENSRNOG00000016273	1 retrocopy	retro_rnor_1679,
Sus scrofa	ENSSSCG00000026446	6 retrocopies	retro_sscr_1075, retro_sscr_229, retro_sscr_230, retro_sscr_309, retro_sscr_335, retro_sscr_914,
Ictidomys tridecemlineatus	ENSSTOG00000008343	1 retrocopy	retro_itri_1026 ,
Tupaia belangeri	ENSTBEG00000017418	8 retrocopies	retro_tbel_1377, retro_tbel_1875, retro_tbel_2479, retro_tbel_2516, retro_tbel_3373, retro_tbel_3703, retro_tbel_401, retro_tbel_999,
Tursiops truncatus	ENSTTRG00000001198	5 retrocopies	retro_ttru_1110, retro_ttru_1771, retro_ttru_1903, retro_ttru_396, retro_ttru_550,