RetrogeneDB ID: retro_itri_1444

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393488.1:1647630..1648274(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSSTOG00000025125
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_itri_1444
ACACTCATGGACTGTGTGATTGTGAGCGATCCAAACACCAAAAGTTCCAGGGGATTTGGGTTTGTCACTTATTCATTGTG
GAGGAAGTGGATGCAGCCATGAATGCAAGACCACACAAGGTGGATGAGAGAGTTGTGGAACCAAAGAGAGCTGTCTCAAA
GAAAATTTCAAAAACCAGGGGTCCACTTAACTGTGAAAAAGATCTTTGTTGGTGCCATTAAAGAAGATACTGAAGAACAT
CACCTATAAGATTATTTTGAACAATATGGGAAAATTGAAGTTATTGAAATCATGACTGATGGAAGCAGTGGAAAGAAAAG
GGGCTTTATTTTTGTAACTTTTGATGACCATGACTCTGTGGATAAGATTGTCATTCAGATAAACCAGACTGTGAATGGCC
ACAACTGTGAAGTGAGGAAAGCCCTGTCAAAGCAATGTCTAGTGCTTCATTTCGCCAACATGGTCAAGGTGGTTCTGGAT
ACTTTGTTGGTGGTCATGGAGGTGGTTTTGATGGAAATGGCAAATTTGGTCATTGGGGAAACTTCAGTGGTTGTGGTACC
TCTGATGGAAGCTGTGGTGGTGGTGGATATGGTGGCATTAGAGATGGCTACAGTGGATTTGATAATGATGGAAGCAATTT
TGGA

Alignment

ORF - retro_itri_1444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.51 %
• Parental protein coverage: 57.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLTDCVVMRDPQTKRSRGFGFVTYSC-VEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKK-
          TL.DCV...DP.TK.SRGFGFVTYS..VEEVDAAM.ARPHKVD.RVVEPKRAVS...S.K....L...K.
Retrocopy TLMDCVIVSDPNTKSSRGFGFVTYSL<VEEVDAAMNARPHKVDERVVEPKRAVSKKIS-KTRGPLNCEK>

Parental  IFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCE
          IFVG.IKEDTEE..L.DYFE.YGKIE.IE.M.D..SGKKRGF.FVTFDDHD.VDKIV.Q...T.NGHNCE
Retrocopy IFVGAIKEDTEEHHL*DYFEQYGKIEVIEIMTDGSSGKKRGFIFVTFDDHDSVDKIVIQINQTVNGHNCE

Parental  VKKALSKQEM-QSAGSQRGRGGGSGNFMGRGGNFGGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGG
          V.KALSKQ........Q.G..GGSG.F.G..G....G.G.FG..GNF.G.G...G..GG..G.YGG...G
Retrocopy VRKALSKQCL<SASFRQHGQ-GGSGYFVGGHGGGFDGNGKFGHWGNFSGCGTSDGSCGG--GGYGGIRDG

Parental  YNGFGGDGGNYG
          Y.GF..DG.N.G
Retrocopy YSGFDNDGSNFG

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_1444 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1444 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 19 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444 , retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,