RetrogeneDB ID: retro_itri_25

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393336.1:8533008..8534271(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027748
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSSTOG00000012612
• Aliases: None
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_itri_25
ATGTCTTCCTTCCGCTTTGTGTGCCAGCGATGCAACCGGCCGCTGAAAGGTGATGAATCCATGGAGATGCCCAGCTCTGG
GCAGGGGGAGCCAGGAGAAGCGCAAGAGGATGGTGCCCGCTCCATGGAGAAGACAGACGGTGGGGAGCCACAAGTCAGTG
CCTCCAGAACCCTTCCTGATGATGTGGGGATGTCGGAGCAAAGCAGCAGCAATTTCATCTTGCTTGGTAAGATCACCTCC
TTGAGAACTTTGAGTAGCATCCAGAAGACCACCGCAGAAATGTTTGACATCCTCTCTGGTCAAAAAGAGATGGATCTTCC
ACTGTGCGAGGAATGTACTGACAATTTTCTAAAGCAGCTGGATTCCCAAATTGCCCTCACAGAACTGGATGAACAGATCT
ATAGACGCTATCTGGAAACCAAGGTGCTGAAGGATGAGGACCAAAGAGAGACACTACAGATGGAGTTGCAGGCCCTGGAG
CTGGAGGAGGCCAAGCTGGCCCAGGAGCTGAAGGATGTGGATGAGAACCATGCAAGAATAGCAGCGGATCTCAGGGCAGC
CCAGGCAGAGACGGTGGAGCTGCAACTGCAGGAGAGACAGCATCTGAGGGACTTCAGTCATCTGAAGTGGCAGCAGCAGG
AACTGTCCGACCAGCTGACAAGTGTGGAGAACCAGCTGTGGTACGCGAGTGTCCAGCTGGACCGGCTGAAGAAGACCAAC
ATCTTCGATGCCACATTTGAGATCAGGGAGGAGGGAACTTTGGGTATCATCAATAACTTCAGATTGGGCCGCCTCCCCAG
CGTCCCCGTGGGCTGGAATGAGATTAACGCTGCCTGGGGACAGGCAGCTTTGCTGCTCCTGACCCTGTCCAAAGCAATCG
GGCTGCAGTTTCAGAGGTATCAACTCATGGCCTGTGGAAACCATTCCTATTTGAAGTCTTTAACCGGTGACTGTGCTGAC
CTGCCCCTGTTTGCTGATGGGAGAGAAAATGTTTTCTGGAATAATACCTTTGACCAGGCCATCTTGGCTTTCCTGGACTG
CCTGCAGCAGTTCGAGGAAGAGGCTGAGAAACAGGCGGGGGATCTCTGCCTGCCCTACAGGATCCTCCTGGAGGAAGGCC
TGATAGAGGACCCCACAGGCAGCGGGGAATGGTATTCTGTCAGGACTCATCTGAACACAGAGGAGCAGTGGACAAAGGCA
CTCAAGTTAATGCTTCTCAATTTGAAGAGAAGTCTTTCTTGGGTTTCCTCGAGGTACCATCAA

Alignment

ORF - retro_itri_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.75 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATAQAKPGDTQEEEANSGEEPFIETRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKV
          ...Q..PG..QE..A.S.E.......Q...SR...P....MS..S...F.L.G..........LS...K.
Retrocopy SSGQGEPGEAQEDGARSMEKTDGGEPQVSASRT-LPDDVGMSEQSSSNFILLGKIT---SLRTLSSIQKT

Parental  TGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKCCLEILEQMNEDDSEQLQRELKELA
          T...FDI.SGQ...D.PLCEECTD..L.QLD.Q...TE...Q.Y...LE......ED..E.LQ.EL..L.
Retrocopy TAEMFDILSGQKEMDLPLCEECTDNFLKQLDSQIALTELDEQIYRRYLETKVLKDEDQRETLQMELQALE

Parental  LEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQMRYAQ
          LEE..L.QEL.DV..N....A..L...QAE...L...E.Q..R..S..K.QQ.EL.D.L.SVENQ..YA.
Retrocopy LEEAKLAQELKDVDENHARIAADLRAAQAETVELQLQERQHLRDFSHLKWQQQELSDQLTSVENQLWYAS

Parental  MQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMGLKFQRY
          .QLD.LKKTN.F.ATF.I...G..G.INNFRLGRLPSVPV.WNEINAAWGQ..LLL..L....GL.FQRY
Retrocopy VQLDRLKKTNIFDATFEIREEGTLGIINNFRLGRLPSVPVGWNEINAAWGQAALLLLTLSKAIGLQFQRY

Parental  RLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDV
          .L...GNHSYL.SLT.....LPL...G....FW.N.FD.A..AFLDC.QQF.EE.EK.....CLPYR...
Retrocopy QLMACGNHSYLKSLTGDCADLPLFADGRENVFWNNTFDQAILAFLDCLQQFEEEAEKQAGDLCLPYRILL

Parental  EKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFY
          E.G.IED..GSG..YS..T..N.EEQWTKALK.ML.NLK..L.WVSS...
Retrocopy EEGLIEDPTGSGEWYSVRTHLNTEEQWTKALKLMLLNLKRSLSWVSSRYH

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_25 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_25 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25 ,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,