RetrogeneDB ID: retro_itri_157

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393629.1:532036..533920(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000014053
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBQLN1
• Ensembl ID: ENSSTOG00000013462
• Aliases: None
• Description: ubiquilin 1 [Source:HGNC Symbol;Acc:12508]

Sequence

>retro_itri_157
ATGGCTGAGAACGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGTCCTGCTGCGGCCCAAGGCTCGGCCGCTGCCCC
GGCTGAGCCCAAAATCATCAAAGTCACTGTGAAGACCCCCAAAGAGAAAGAGGAGTTCGCGGTGCCTGAGAATAGCTCGG
TCCAGCAGTTTAAGGAAGCGATTTCAAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCTGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCATGGCATCCATGATGGACTGACTGTTCACCTTGTCATCAAAAGCCAGAATCG
ACCTCAGGGCCAGTCCACCACACAGCCTAGCAGTGCCGCGGGAACTACTACTACCACCACCACGGCGTCGACTCCCAGGA
GTAACTCCACACCTACTACCACAAATAGCAGCCCGTTCGGGTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGCAGCCTT
GGTTTGAGCTCGACCAACTTCTCTGAGCTCCAGAACCAGATGCAGCAGCAGCTCATGGCCAGTCCTGAGATGATGATTCA
AATCATGGAAAATCCCTTTGTTCAGAGCATGCTTTCGAATCCTGATCTGATGAGGCAGCTCATTATGGCCAATCCACAGA
TGCAACAATTGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACTCTCGAAATC
GCCAGGAATCCAGCCATGATGCAAGAGATGATGAGAAATCAAGATCTGGCTCTCAGCAATCTCGAAAGCATCCCAGGTGG
CTACAATGCTCTACGGCGCATGTACACTGACATTCAAGAACCCATGCTGAATGCCGCACAAGAGCAGTTTGGGGGTAATC
CATTTGCCTCAGTGGGGAGCAGTTCCTCCTCCGGGGAAGGTACTCAGCCTTCCCGCACAGAAAATCGGGATCCACTGCCC
AATCCATGGGCGCCACCGTCGACTACCCAGAGTTCTGCGACCACCAGTACCACCACAAGCAGTGGCAGTGGGTCTGGCAG
TAGCTCCAGTAATACTGCTGGGAACACTGTGGCTGCAGCTAATTATGTCGCTAGCATTTTCAGTACCCCAGGAATGCAGA
GCCTGCTGCAACAGATAACTGAAAACCCCCAGCTGATTCAGAATATGCTGTCCGCACCCTACATGAGAAGCATGATGCAG
TCGCTGAGCCAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCACTGTTTACTGCAAATCCTCAGCTGCAGGA
GCAGATGCGTCCTCAGCTCCCAGCTTTCCTGCAGCAGATGCAGAATCCAGACACGCTATCAGCCATGTCAAACCCAAGAG
CAATGCAGGCTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTCATTCCAAGCTTCACT
CCAGGTGTGGGGGTGGGGGTGCTGGGAACCGCCATAGGCCCTGTAGGCCCAGTCACTCCCATAGGCCCCATAGGCCCTAT
AGTCCCTTTTACCCCCATAGGCCCCATTGGGCCCATAGGACCCACTGGCCCTGCAGGGCCCCCTGGCTCCACCGGCTCTG
GCGGCCCCACTGCACCCACTGTGTCCAGCTCTGCACCCAGTGAAACCACCACTCCAACATCAGAATCTGGACCCAACCAG
CAGTTCATTCAGCAAATGGTGCAGGCTCTGGCTGGAGCAAATCCTCCACAGCTGCCGAATCCAGAAGTCAGATTTCAGCA
GCAACTGGAACAGCTCAACGCCATGGGGTTCTTAAACCGTGAAGCAAACTTGCAGGCCCTAATAGCAACAGGAGGCGACA
TCAATGCAGCCATTGAGAGGCTGCTGGGCTCCCAGCCATCGTAA

Alignment

ORF - retro_itri_157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 80.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLIMANPQMQQL
          LG.LGGLAGLSSLGL..TNFSELQ.QMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLIMANPQMQQL
Retrocopy LGSLGGLAGLSSLGLSSTNFSELQNQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIMANPQMQQL

Parental  IQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQEPMLSAAQ
          IQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQEPML.AAQ
Retrocopy IQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQ

Parental  EQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQASQSSSASSGTTNTVSGTAGSTTSGTAGQST
          EQFGGNPFAS..S..SSGEG.QPSRTENRDPLPNPWAP.....SSA...TT.......GS..S.TAG...
Retrocopy EQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPSTTQSSATTSTTTSSGSGSGSSSSNTAGNTV

Parental  TGPNLVPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLNNPLFAGNP
          ...N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN.PLF..NP
Retrocopy AAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLNSPLFTANP

Parental  QLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPNLGALGNTGGSS
          QLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTP..G..G..G...
Retrocopy QLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG-VGVLGTAI

Parental  GTNGSST
          G..G..T
Retrocopy GPVGPVT

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_157 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_157 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014827	2 retrocopies	retro_btau_1087, retro_btau_188,
Canis familiaris	ENSCAFG00000001435	1 retrocopy	retro_cfam_236,
Callithrix jacchus	ENSCJAG00000003609	2 retrocopies	retro_cjac_3977, retro_cjac_4067,
Cavia porcellus	ENSCPOG00000004849	1 retrocopy	retro_cpor_113,
Dasypus novemcinctus	ENSDNOG00000012687	1 retrocopy	retro_dnov_14,
Dipodomys ordii	ENSDORG00000015266	1 retrocopy	retro_dord_680,
Equus caballus	ENSECAG00000019110	1 retrocopy	retro_ecab_1063,
Echinops telfairi	ENSETEG00000002822	1 retrocopy	retro_etel_39,
Felis catus	ENSFCAG00000015049	1 retrocopy	retro_fcat_83,
Homo sapiens	ENSG00000135018	1 retrocopy	retro_hsap_58,
Myotis lucifugus	ENSMLUG00000002036	2 retrocopies	retro_mluc_1774, retro_mluc_33,
Mustela putorius furo	ENSMPUG00000002028	1 retrocopy	retro_mputfur_55,
Mus musculus	ENSMUSG00000005312	1 retrocopy	retro_mmus_83,
Nomascus leucogenys	ENSNLEG00000003306	1 retrocopy	retro_nleu_31,
Otolemur garnettii	ENSOGAG00000012947	1 retrocopy	retro_ogar_276,
Pongo abelii	ENSPPYG00000019323	1 retrocopy	retro_pabe_87,
Pan troglodytes	ENSPTRG00000021055	1 retrocopy	retro_ptro_93,
Rattus norvegicus	ENSRNOG00000019282	1 retrocopy	retro_rnor_339,
Ictidomys tridecemlineatus	ENSSTOG00000013462	1 retrocopy	retro_itri_157 ,
Tursiops truncatus	ENSTTRG00000004696	1 retrocopy	retro_ttru_1475,