RetrogeneDB ID: retro_itri_1614

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393574.1:373340..373876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF4
• Ensembl ID: ENSSTOG00000019470
• Aliases: None
• Description: ADP-ribosylation factor 4 [Source:HGNC Symbol;Acc:655]

Sequence

>retro_itri_1614
ATGGGCCTCACCATCTCTTCTCTGTTCTCCCGCCTCTTTGGCAAGAAGCAGATGCGTATTTTGATGGTTGGATTGGATGC
TGCTGGCAAGATGACCATTAAACTGAAGTTAGGGGAGACAGTCCCCACCATTCCTACCATTGGTTTTTAATGTGGAAACA
GTAGAGTATAAGAACATGTGTTTCACTGTATGGGATGTTGGGGGTCAAGATAAAATCAGGCCTCTCTGGAGGCATTACTT
CCAGAATAGCCAGGGTCTTATTTTTGTGCTAGATAGCAATGATGGTGAAAGAATTCAGGAAGGAGCCCAAGTCCTGCAGA
AAATGCTTGGGGAAGATGAGCTGCAAGATGCAGTGCTGTTGCTTTTTGCAAACAAACAGGATTTGCCAAATGCTACGGCT
ATCCGGGAAATGACAGATTAAATGAGGCCTTCAGTCTCTCCATAACAGAACATGGTATGTTCAAGCCGCTTGTGCTACAC
AAGGAACTGGTCTGTATGAGGGACTTGATTGGCTGTCGAACGAGCTTTCAAAACGT

Alignment

ORF - retro_itri_1614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGLTISSLFSRLFGKKQMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGF-NVETVEYKNICFTVWDVG
          MGLTISSLFSRLFGKKQMRILMVGLDAAGK.TI..KLKLGE.V.TIPTIGF.NVETVEYKN.CFTVWDVG
Retrocopy MGLTISSLFSRLFGKKQMRILMVGLDAAGKMTI--KLKLGETVPTIPTIGF>NVETVEYKNMCFTVWDVG

Parental  GQDKIRPLWRHYFQNTQGLIFVVDSNDRERIQEGAQVLQKMLEEDELQDAVLLLFANKQDLPNAMAISEM
          GQDKIRPLWRHYFQN.QGLIFV.DSND.ERIQEGAQVLQKML.EDELQDAVLLLFANKQDLPNA.AI.EM
Retrocopy GQDKIRPLWRHYFQNSQGLIFVLDSNDGERIQEGAQVLQKMLGEDELQDAVLLLFANKQDLPNATAIREM

Parental  TD-KLGLQSLRNRTWYVQATCATQGTGLYEGLDWLSNELSKR
          TD.K.GLQSL.NRTWYVQA.CATQGTGLYEGLDWLSNELSKR
Retrocopy TD>K*GLQSLHNRTWYVQAACATQGTGLYEGLDWLSNELSKR

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_1614 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1614 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 28 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016069	1 retrocopy	retro_btau_542,
Choloepus hoffmanni	ENSCHOG00000006427	4 retrocopies	retro_chof_1024, retro_chof_1807, retro_chof_2368, retro_chof_36,
Ciona intestinalis	ENSCING00000021790	1 retrocopy	retro_cint_10,
Callithrix jacchus	ENSCJAG00000019922	1 retrocopy	retro_cjac_507,
Cavia porcellus	ENSCPOG00000010334	1 retrocopy	retro_cpor_1261,
Dipodomys ordii	ENSDORG00000004312	1 retrocopy	retro_dord_731,
Homo sapiens	ENSG00000168374	2 retrocopies	retro_hsap_1296, retro_hsap_4221,
Gorilla gorilla	ENSGGOG00000000294	1 retrocopy	retro_ggor_1552,
Microcebus murinus	ENSMICG00000002015	3 retrocopies	retro_mmur_1528, retro_mmur_1558, retro_mmur_360,
Myotis lucifugus	ENSMLUG00000007990	1 retrocopy	retro_mluc_2272,
Macaca mulatta	ENSMMUG00000018617	1 retrocopy	retro_mmul_50,
Monodelphis domestica	ENSMODG00000000185	1 retrocopy	retro_mdom_1538,
Nomascus leucogenys	ENSNLEG00000007270	3 retrocopies	retro_nleu_2106, retro_nleu_2703, retro_nleu_2704,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Otolemur garnettii	ENSOGAG00000012034	4 retrocopies	retro_ogar_1407, retro_ogar_1501, retro_ogar_2963, retro_ogar_764,
Pongo abelii	ENSPPYG00000013768	3 retrocopies	retro_pabe_1013, retro_pabe_1075, retro_pabe_3451,
Pan troglodytes	ENSPTRG00000015051	2 retrocopies	retro_ptro_2866, retro_ptro_888,
Rattus norvegicus	ENSRNOG00000012623	2 retrocopies	retro_rnor_1036, retro_rnor_1884,
Sorex araneus	ENSSARG00000009272	1 retrocopy	retro_sara_681,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Ictidomys tridecemlineatus	ENSSTOG00000013990	1 retrocopy	retro_itri_659,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614 ,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883,
Tupaia belangeri	ENSTBEG00000007415	1 retrocopy	retro_tbel_2075,
Tarsius syrichta	ENSTSYG00000009748	1 retrocopy	retro_tsyr_2059,
Tursiops truncatus	ENSTTRG00000015381	1 retrocopy	retro_ttru_284,
Vicugna pacos	ENSVPAG00000003891	1 retrocopy	retro_vpac_459,