RetrogeneDB ID: retro_itri_1834

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393969.1:17743..18851(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSSTOG00000001660
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_itri_1834
ATGTCCCTGCATCAGTTTTTACTAGAGCCAATCACCTATCATGCTTGGAACAGGGAGCATAACCAGATTGCCCTTAGCCC
CAATAATCATGAAGTGCACATCTATAAGAAGTACGGGGAGCCAGTGGCTGAAAGCTCATGAACTCAAGGAGTACAATGGA
CACATCACAGGTATTGTCTAGGCTCCCAAGAGTGACCACATCCTCACTTGTGGGGCAGACTGCAATGCCTATGTCTGGAG
TCAGAAAGATGGCGTCTGGAAGCCCACCCTGGTGATCCTGAGGATCAATCTTGCAGCCACTTTTGTGAAATAGTCCCCTC
AAGAGAACAAATTTGCTGTGGGAAATGGAGCACGACTCATTTCTGTTTGCTACTTCCAGTCTGAAAATGACTGATGGGTA
AGCAAGCACATTAAAAAGCCAATTTGCTCCACGATCCTCAACTTGGATTGCCATCCCAACAACTTTTGCTGGCAGCAGGA
TCGTGCGACTTCAAATGCAGAGTATTTTCTGCCTACATTAAAGAAGTGGATGAAAAGCCAGCCAGTGCACCCTGGGGCAG
CAAGATGCCTTTTGGCCAGTTGATGTCAGAGTTTGGTGGCAGTGGCACTGGCGGCTGGGTCCATGGGGTCAACTTCTCTG
CCAGTGGGAGCTATCTGGCCTGGGTCAGCCAGACAGCACCGTGTCTGTTGCTGATGCCTCAAAAAATATCCAGGTCTCAA
CTCTGAAAACGGAGTTCCTGCCACTCCTGAGTGTATCATTTGTCTCGAAGAATAGTGTTGTGGCTGCTGACCATGACTTC
TGCCTGTTGCTGTTTAAATATAATGACCACGGCTGTTTGACCTTTGTCTCCAAGCTGGATATTCTAAAGCAGAGTATCCA
ATGCAACATGTGTGTCATGGAAAGCTTCCATAACATGGACAAGAGGGCCACCACCCAGGACTGCAATACAGCCTTGGAAA
CGCTGCACCAGAACAGCATCACTCAAGTGTCTATTTATGAGGTGGACAAACAAGATTGTCGCAAATTTTGCACTACTGGC
ATCATGGAACCATGACAATTTGGGATTTCAAGACCTTATAGTCTTTGATCCAGGGTCTCCGGATAATG

Alignment

ORF - retro_itri_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKK-NGSQWVKAHELKEHNGHITGIDWAPKSDRIVT
          MSLHQFLLEPIT.HAWNR...QIALSPNNHEVHIYKK..GSQW.KAHELKE.NGHITGI..APKSD.I.T
Retrocopy MSLHQFLLEPITYHAWNREHNQIALSPNNHEVHIYKK>TGSQWLKAHELKEYNGHITGIV*APKSDHILT

Parental  CGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKK
          CGAD.NAYVWSQKDGVWKPTLVILRIN.AATFVK.SP.ENKFAVG.GARLISVCYF.SEND.WVSKHIKK
Retrocopy CGADCNAYVWSQKDGVWKPTLVILRINLAATFVK*SPQENKFAVGNGARLISVCYFQSEND*WVSKHIKK

Parental  PIRSTVLSLDWHPNN-VLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVH
          PI.ST.L.LD.HPNN..LLAAGSCDFKCRVFSAYIKEVDEKPAS.PWGSKMPFGQLMSEFGGSGTGGWVH
Retrocopy PICSTILNLDCHPNN<LLLAAGSCDFKCRVFSAYIKEVDEKPASAPWGSKMPFGQLMSEFGGSGTGGWVH

Parental  GVSFSASGSRLAWVSH-DSTVSVADASKSVQVSTLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDR
          GV.FSASGS.LAWVS..DSTVSVADASK..QVSTLKTEFLPLLSVSFVS.NSVVAA.HD.C..LF.Y.D.
Retrocopy GVNFSASGSYLAWVSQ<DSTVSVADASKNIQVSTLKTEFLPLLSVSFVSKNSVVAADHDFCLLLFKYNDH

Parental  GCLTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTG
          GCLTFVSKLDI.KQSIQ.NM..ME.F.NMDKRATT.D.NTALETLHQNSITQVSIYEVDKQDCRKFCTTG
Retrocopy GCLTFVSKLDILKQSIQCNMCVMESFHNMDKRATTQDCNTALETLHQNSITQVSIYEVDKQDCRKFCTTG

Parental  I-DGAMTIWDFKTLESSIQGLRIM
          I..G.MTIWDFKTL.S.IQGLRIM
Retrocopy I<HGTMTIWDFKTL*SLIQGLRIM

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_1834 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1834 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 21 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834 ,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,