RetrogeneDB ID: retro_itri_1083

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393372.1:1499840..1500815(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLUL
• Ensembl ID: ENSSTOG00000014529
• Aliases: None
• Description: glutamate-ammonia ligase [Source:HGNC Symbol;Acc:4341]

Sequence

>retro_itri_1083
TTGAACAAAGGCATCAAGTAGGGGTATATATCCCTGCCTCAAGTAAGAAAGCCCAAGCTATATATATCTGGATTGATGGC
CCTGGAGAAGGACTTCACTGTAAGACCCACACCCTGGACTCTGAGCCCAAGAGTGTAGAGAGTTGCCTGAGTGGAATTTT
GATGGCTATAGTACTTTTCGGTCTAAAGGCTCCTATAATGACATGTATCTTGTACCTGCTACCATGTTTCAGGACCCTTT
CCCCAAGGATCCCAACACACTGGTGTTCTGTGAAGTTTTCAAGTATAACCGAAAGCCTGCAGAGACCAATTTAAGGCACA
CCCATAAACTGATAATGGATATGGTGAGCAACCAGCATCCTTGGTTTGGAATGGAGCAGGAATACACTCTCAAGGGCACA
GATGGCCACCCTTTCCGTTGGTCTTCCAATGGCTTTTCTGGTCCCCAAGGTCCTTATTACTGTGGTGTGGCACCAGACAA
CGCCTACTGCAGGGATACCGTGGAGGCTTATTACCAGGCCTGCTTGTATGCTGGAGTCAAGATTACGGGGACAAATGCTG
AGATCATGCCTGCCCCGTGGGAATTCCAAATAGGACATTGTGAAGGAATCCACATGGGAGATCATCTCTAGGTGGCCCGT
TTCATCCTGCATCACGTATGTGAAGACTTTAGAATGATAGCTACTTTTGATCCCAAGCCCATTCCTGGGATCTGACATGA
TTCAGGCTGCCCCACCAACTTTAGTACCAAAGGCCACGAGGGAGAGATTGATCTCAAGTACATTGAGGAGGCCATTGAGA
AACTAAGCAAGCAGCGCCAGTACCCCCACATTCATGCCTGAGCTCCCAAGGGGGCCTGGACAATGCCTGGCGTCTAACTG
GATTCCACAAAACTTCCCACATCGATGACTTCTCTGCTGGCACGGCCAACCATAGTGCCAGCATCTGCATTCCCCTCGCT
GTCAGCAGAAGAAGG

Alignment

ORF - retro_itri_1083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.51 %
• Parental protein coverage: 82.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNKGIKQVYMSLPQ-GEKVQAMYIWIDGTGEGLRCKTRTLDSEPKSVE-ELPEWNFDGSSTFQSEGSNSD
          LNKGIK..Y.SLPQ...K.QA.YIWIDG.GEGL.CKT.TLDSEPKSVE.ELPEWNFDG.STF.S.GS..D
Retrocopy LNKGIK*GYISLPQ<SKKAQAIYIWIDGPGEGLHCKTHTLDSEPKSVE<ELPEWNFDGYSTFRSKGSYND

Parental  MYLVPAAMFRDPFRKDPNKLVFCEVFKYNRKPAETNLRHTCKRIMEMVSNQHPWFGMEQEYTLMGTDGHP
          MYLVPA.MF.DPF.KDPN.LVFCEVFKYNRKPAETNLRHT.K.IM.MVSNQHPWFGMEQEYTL.GTDGHP
Retrocopy MYLVPATMFQDPFPKDPNTLVFCEVFKYNRKPAETNLRHTHKLIMDMVSNQHPWFGMEQEYTLKGTDGHP

Parental  FGWPSNGFPGPQGPYYCGVGADKAYGRDIVEAHYRACLYAGVMITGTNAEVMPAQWEFQIGPCEGIHMGD
          F.W.SNGF.GPQGPYYCGV..D.AY.RD.VEA.Y.ACLYAGV.ITGTNAE.MPA.WEFQIG.CEGIHMGD
Retrocopy FRWSSNGFSGPQGPYYCGVAPDNAYCRDTVEAYYQACLYAGVKITGTNAEIMPAPWEFQIGHCEGIHMGD

Parental  HLWVARFILHRVCEDFGVIATFDPKPIPGNWNGAGCHTNFSTKAMREENGLKYIEEAIEKLSKRHQY-HI
          HL.VARFILH.VCEDF..IATFDPKPIPG.....GC.TNFSTK....E..LKYIEEAIEKLSK..QY.HI
Retrocopy HL*VARFILHHVCEDFRMIATFDPKPIPGI*HDSGCPTNFSTKGHEGEIDLKYIEEAIEKLSKQRQYPHI

Parental  RAYDPK-GGLDNARRLTGFHETSNINDFSAGVANRSASIRIPRTVGQER
          .A..PK.GGLDNA.RLTGFH.TS.I.DFSAG.AN.SASI.IP..V...R
Retrocopy HA*APK<GGLDNAWRLTGFHKTSHIDDFSAGTANHSASICIPLAVSRRR

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_1083 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1083 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 24 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013631	4 retrocopies	retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris	ENSCAFG00000013102	2 retrocopies	retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus	ENSCJAG00000004654	1 retrocopy	retro_cjac_2837,
Dasypus novemcinctus	ENSDNOG00000013948	4 retrocopies	retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus	ENSECAG00000015865	1 retrocopy	retro_ecab_979,
Echinops telfairi	ENSETEG00000008329	3 retrocopies	retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus	ENSFCAG00000010551	1 retrocopy	retro_fcat_1811,
Homo sapiens	ENSG00000135821	4 retrocopies	retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla	ENSGGOG00000024712	3 retrocopies	retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana	ENSLAFG00000000700	1 retrocopy	retro_lafr_196,
Macropus eugenii	ENSMEUG00000001774	6 retrocopies	retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta	ENSMMUG00000022884	2 retrocopies	retro_mmul_2047, retro_mmul_954,
Monodelphis domestica	ENSMODG00000006787	4 retrocopies	retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus	ENSMUSG00000026473	3 retrocopies	retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys	ENSNLEG00000018007	3 retrocopies	retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii	ENSPPYG00000000440	1 retrocopy	retro_pabe_2698,
Pan troglodytes	ENSPTRG00000001751	4 retrocopies	retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii	ENSSHAG00000000116	1 retrocopy	retro_shar_553,
Sus scrofa	ENSSSCG00000015545	1 retrocopy	retro_sscr_726,
Ictidomys tridecemlineatus	ENSSTOG00000014529	2 retrocopies	retro_itri_1083 , retro_itri_743,
Tupaia belangeri	ENSTBEG00000003522	3 retrocopies	retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta	ENSTSYG00000002066	1 retrocopy	retro_tsyr_385,
Tursiops truncatus	ENSTTRG00000010781	1 retrocopy	retro_ttru_543,
Drosophila melanogaster	FBgn0001145	1 retrocopy	retro_dmel_44,