RetrogeneDB ID: retro_itri_459

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:2501514..2501978(+)
• Located in intron of: ENSSTOG00000009068

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTF3L4
• Ensembl ID: ENSSTOG00000006129
• Aliases: None
• Description: basic transcription factor 3-like 4 [Source:HGNC Symbol;Acc:30547]

Sequence

>retro_itri_459
ATGAACCAGGAAAAACTCGCCAAACTGCAGGCACAAGTGCACATTGGTGGGGAAGGAACTACTCACAGAAAGAAGGTGGT
TCATAGAACAGCTACAGCAGATGATAAAAGACTTCAGTTCTCCTTAAAGAACTTAGGGGTAAACAATGTCTCTGGTATTA
AAGAGTTGAATATGTTTACAAACCAAGGAACAGTGATCCACTTTAACAACCCTGAAGTTCAGGCGTCTCTGGCCGCAAAC
ACTTTCACCATTACAGGCCATGCTGGGACAAAGCAACTACAGAAATACTACCCAGCATCTTAAACCAACTTGGTGCAGAC
CGTCTGACTAGTTGAAGGAGACTGGCTGAGCTCTGCTCAAACAGTCTGGATGGAAAAGCATCACTTACTGCTGAAGAGGA
TGATGATGATGAAGTTCCAGATCTTGTGCAAAATTTTGTTGAGGCTTCTAAGAATGAGACAAAC

Alignment

ORF - retro_itri_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFN
          MNQEKLAKLQAQV.IGG.GT..R.KKVVHRTATADDK.LQ.SLK.L.VNN..GI.E.NM....GTVIHFN
Retrocopy MNQEKLAKLQAQVHIGGEGTTHR-KKVVHRTATADDKRLQFSLKNLGVNNVSGIKELNMFTNQGTVIHFN

Parental  NPKVQASLSANTFAITGHAEAKPI-TEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEED
          NP.VQASL.ANTF.ITGHA..K...TE.LP.IL.QLGAD.LTS.R.LAE......LD.KA.........D
Retrocopy NPEVQASLAANTFTITGHAGTKQL<TEILPSILNQLGADRLTS*RRLAELCSNS-LDGKASLTAE-EDDD

Parental  DDVPDLVENFDEASKNEAN
          D.VPDLV.NF.EASKNE.N
Retrocopy DEVPDLVQNFVEASKNETN

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_459 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_459 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 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021582	4 retrocopies	retro_cjac_2000, retro_cjac_2929, retro_cjac_4160, retro_cjac_451,
Cavia porcellus	ENSCPOG00000004006	1 retrocopy	retro_cpor_908,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dasypus novemcinctus	ENSDNOG00000003181	4 retrocopies	retro_dnov_1690, retro_dnov_1928, retro_dnov_2672, retro_dnov_921,
Echinops telfairi	ENSETEG00000011923	11 retrocopies	retro_etel_1017, retro_etel_1167, retro_etel_1207, retro_etel_1409, retro_etel_1990, retro_etel_2113, retro_etel_2203, retro_etel_291, retro_etel_663, retro_etel_804, retro_etel_953,
Loxodonta africana	ENSLAFG00000016124	3 retrocopies	retro_lafr_206, retro_lafr_769, retro_lafr_947,
Macropus eugenii	ENSMEUG00000006135	10 retrocopies	retro_meug_1114, retro_meug_1164, retro_meug_1333, retro_meug_1395, retro_meug_1512, retro_meug_1663, retro_meug_2008, retro_meug_298, retro_meug_903, retro_meug_966,
Myotis lucifugus	ENSMLUG00000016884	1 retrocopy	retro_mluc_912,
Macaca mulatta	ENSMMUG00000003636	1 retrocopy	retro_mmul_59,
Monodelphis domestica	ENSMODG00000000770	2 retrocopies	retro_mdom_33, retro_mdom_992,
Mus musculus	ENSMUSG00000028568	2 retrocopies	retro_mmus_1134, retro_mmus_2743,
Oryctolagus cuniculus	ENSOCUG00000001517	3 retrocopies	retro_ocun_1001, retro_ocun_1412, retro_ocun_1912,
Otolemur garnettii	ENSOGAG00000030256	2 retrocopies	retro_ogar_2759, retro_ogar_570,
Procavia capensis	ENSPCAG00000006428	3 retrocopies	retro_pcap_129, retro_pcap_307, retro_pcap_373,
Pongo abelii	ENSPPYG00000001353	2 retrocopies	retro_pabe_1850, retro_pabe_3010,
Rattus norvegicus	ENSRNOG00000008512	8 retrocopies	retro_rnor_1113, retro_rnor_1666, retro_rnor_1870, retro_rnor_1871, retro_rnor_1872, retro_rnor_537, retro_rnor_760, retro_rnor_998,
Ictidomys tridecemlineatus	ENSSTOG00000006129	6 retrocopies	retro_itri_1309, retro_itri_402, retro_itri_459 , retro_itri_541, retro_itri_701, retro_itri_810,
Tarsius syrichta	ENSTSYG00000013635	3 retrocopies	retro_tsyr_1576, retro_tsyr_1822, retro_tsyr_2045,