RetrogeneDB ID: retro_itri_215

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:46016725..46017850(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000011472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015459
• Aliases: None
• Description: None

Sequence

>retro_itri_215
ATGTCGTCCCATGAAGGACCAGTGGTGGCCCAGGGCAATGGGGCTCCTGCTAGTAACAAGCAAACGAACAGAGTAGAACT
GGCTAAGCTGAGACCTGTGCCCAAAGAGAAGGGCAAGCGGGTAACTGCGAACCCAGACAAAGCTGAAGAGGGGCAAAGGT
GCCCACTGCCCAAGGAAGAAGAGGAGGAGGTACCCGTCCTGAAGCTCCCCCTGCAGGCTCACCATGCCATGGAGAAGATG
GAGGAGTTCGTGCATAAGGTCTGGGAGGGACACTGGAGCGTCATCCCTTTTGAGATGCTCCCTTACTGGCTGAAGCACAA
TAACTATTTGCTACATGGCCACAGACCACCCATGCCCTCCTTTCGGGCTTGCTTTAAGAGCATCTTCCGCATCCACACAG
AGACTGGCAACATCTGGACCCATCTGCTTGGTTTCGTGCTGTTTCTCTTTTTGGGAATCTTGACCATGCTTCGACCAAAT
ATGTACTTCATGGTCCCTCTCCAGGAGAAAGTGGTTTTGGGCATCTTCTTTCTGAGTGTACTCGTGTGCCTCAGCTTCTC
CTGGCTCTTCCACACTGTCTATTGTCATTCAGAGAAAGTCTCTCAGACCTTTTCCAAACTGGACTATTCAGGGATTTCTC
TACTGATTATGGGGGGCTTTGTCCTCTGGCTCTATTACTCCTTTTATTGCGCCCCGCAGCCTCGGCTCATCTACCTCTCC
ATCATCTGTGTCCTGGGCATCTCTTCCATCTTTGTGGCACAGTGGGACCGGTTTGCCACTCCTGAGCACCGGCAAACAAG
AGCAGCAGTGTTCCTGGGACTTGGCCTCAGTGGTGCTGTGCCCGCCATGCACTTGACTATGGCTGAGGGTTTTGTCAAGG
CCATCACAGTGGGCCAGATGGGCTGGTTCTTTCTCACGGCTATAATGTACATCGCTGGAACCGGCTTTTACGCTGCTCGG
ATTCCTGAGCGCTTCTTTCCTGGGAAGTTTGACATATGGTTCCAGTCCCATCAGATTTTCCACAGCCTGGTAGTGGCAGC
AACCTTTGTCCACTTCTATGGGGTCTCCAACCTTCAGGAATTCCGTTATGGCCTGCATGGTGGCTGTACTGATGACTCCC
TTCTC

Alignment

ORF - retro_itri_215 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSHKGTVVAQGNRAPASNRETDSVELAELGPLLEEKGKRVIANPNKAEEEQTCPVPQEEEEEVRVLTLP
          MSSH.G.VVAQGN.APASN..T..VELA.L.P...EKGKRV.ANP.KAEE.Q.CP.P.EEEEEV.VL.LP
Retrocopy MSSHEGPVVAQGNGAPASNKQTNRVELAKLRPVPKEKGKRVTANPDKAEEGQRCPLPKEEEEEVPVLKLP

Parental  LQAHHAMEKMEEFVYKVWEGRWRVIPYDVLPDWLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETGNIWT
          LQAHHAMEKMEEFV.KVWEG.W.VIP...LP.WLK.N.YLLHGHRPPMPSFRACFKSIFRIHTETGNIWT
Retrocopy LQAHHAMEKMEEFVHKVWEGHWSVIPFEMLPYWLKHNNYLLHGHRPPMPSFRACFKSIFRIHTETGNIWT

Parental  HLLGFVLFLFLGILTMLRPNMYFMAPLQEKVVFGMFFLGAVLCLSFSWLFHTVYCHSEKVSRTFSKLDYS
          HLLGFVLFLFLGILTMLRPNMYFM.PLQEKVV.G.FFL....CLSFSWLFHTVYCHSEKVS.TFSKLDYS
Retrocopy HLLGFVLFLFLGILTMLRPNMYFMVPLQEKVVLGIFFLSVLVCLSFSWLFHTVYCHSEKVSQTFSKLDYS

Parental  GIALLIMGSFVPWLYYSFYCSPQPRLIYLSIVCVLGISAIIVAQWDRFATPKHRQTRAGVFLGLGLSGVV
          GI.LLIMG.FV.WLYYSFYC.PQPRLIYLSI.CVLGIS.I.VAQWDRFATP.HRQTRA.VFLGLGLSG.V
Retrocopy GISLLIMGGFVLWLYYSFYCAPQPRLIYLSIICVLGISSIFVAQWDRFATPEHRQTRAAVFLGLGLSGAV

Parental  PTMHFTIAEGFVKATTVGQMGWFFLMAVMYITGAGLYAARIPERFFPGKFDIWFQSHQIFHVLVVAAAFV
          P.MH.T.AEGFVKA.TVGQMGWFFL.A.MYI.G.G.YAARIPERFFPGKFDIWFQSHQIFH.LVVAA.FV
Retrocopy PAMHLTMAEGFVKAITVGQMGWFFLTAIMYIAGTGFYAARIPERFFPGKFDIWFQSHQIFHSLVVAATFV

Parental  HFYGVSNLQEFRYGLEGGCTDDSLL
          HFYGVSNLQEFRYGL.GGCTDDSLL
Retrocopy HFYGVSNLQEFRYGLHGGCTDDSLL

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_215 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_215 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 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012199	1 retrocopy	retro_amel_1853,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Cavia porcellus	ENSCPOG00000000482	1 retrocopy	retro_cpor_470,
Dipodomys ordii	ENSDORG00000006876	1 retrocopy	retro_dord_19,
Felis catus	ENSFCAG00000013565	1 retrocopy	retro_fcat_1514,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277,
Macropus eugenii	ENSMEUG00000015439	1 retrocopy	retro_meug_516,
Microcebus murinus	ENSMICG00000007942	3 retrocopies	retro_mmur_1199, retro_mmur_184, retro_mmur_764,
Myotis lucifugus	ENSMLUG00000016102	2 retrocopies	retro_mluc_1275, retro_mluc_200,
Macaca mulatta	ENSMMUG00000007046	1 retrocopy	retro_mmul_1322,
Mustela putorius furo	ENSMPUG00000011215	1 retrocopy	retro_mputfur_550,
Otolemur garnettii	ENSOGAG00000033821	4 retrocopies	retro_ogar_1558, retro_ogar_1624, retro_ogar_2838, retro_ogar_783,
Ochotona princeps	ENSOPRG00000004528	3 retrocopies	retro_opri_101, retro_opri_1050, retro_opri_392,
Pongo abelii	ENSPPYG00000000342	1 retrocopy	retro_pabe_1072,
Sorex araneus	ENSSARG00000007680	1 retrocopy	retro_sara_25,
Ictidomys tridecemlineatus	ENSSTOG00000015459	3 retrocopies	retro_itri_215 , retro_itri_257, retro_itri_512,
Tupaia belangeri	ENSTBEG00000015149	2 retrocopies	retro_tbel_1501, retro_tbel_1804,
Tarsius syrichta	ENSTSYG00000001491	1 retrocopy	retro_tsyr_125,
Tursiops truncatus	ENSTTRG00000006381	2 retrocopies	retro_ttru_1055, retro_ttru_863,