RetrogeneDB ID: retro_itri_1046

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393363.1:1351858..1353077(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSSTOG00000008945
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 5 [Source:HGNC Symbol;Acc:9552]

Sequence

>retro_itri_1046
ATGGCGCTTGATGGGCCAGGAAAGATGGAACTGGAAGAGGGAAAAGCAGGCAGCAGCGGACTCCATCAATATTATCTGTC
CAAGATTGAAGAACTCCAGCTGATTGTGAATGATAAAAGCCAAAACCTCCAGAGGCTGCAGGTACAGAGGAATAAACTAA
ATGCAAAAGTTCACCTATTGCAGAGAAGCTACAGCTGCTGCAAGAACAGGGCTCCCATGTGGAAGAAGTAGTTCGGGCCA
TGGTTAAGAAGAAAGTGTTGGTCAAGGTACACCCCAAGGGCAAGTTTGTTGTAGATGTGGACAAGAACATCAACATCATG
ATGTGACACTCAATTGTCGAGTGGCCTCTAAGAAATGACAGCTACACTCTGCACAAGATCCTACCTAACAAGGTGGACCC
TCTGGTGTCACTGATGATGGTGGAGAAGGTGCCAGATTCAACTTACAAATGATTGGTGGGCTGGACAAACAAATCAAGGA
GATCAAAGAAGTGATTGAACTGCCAGTGAAGCACCCCGAGCTCTTTGAAGCACTGGGCATTGCACAGCCCAAGGGAGTGC
TGCTGTATGGACCCCCAGGGACAGGGAAGACACTGTTGGCCCAGGCTGTGGCTCATCCTACAGACTGTACCTTTATTCGT
GTCTCTAGCTCTGAATTAGTACAGAAATTCATTGGGGAAGGGGCAAAAATGGGGAGGGAGCTGTTTGTCATGGCACAAAA
ACATGCTCCATCTATTATCTTCATGGATGAAATTGATTCTATTGGCTCTTCATGGCTGGAAGGGGGCTCTGGAGGGGACA
GTGAAATGCAGCGCACAATGCTAGAGCTGCTCAACCAACTGGATGGCTTTGAGGCCACCAAGAATATTAAGATTGTCATG
GCTACTAATAGGATTGATATACTGGATTCTGCACTGCTTCACCCTGGGCGCATTGACAGAAAAATTGAATTCCCACCTCC
CAATGAGGAGGCCCCACTGGACATTTTGAAGATTCATTCTTGGAAAATGAATCTGATCCAAGGGATCAACCTGATAAAAA
TTGCCGAGCTGATGCCAGGAGCATCAGGGGCCGAAGTGAAGGGTGTATGCATAGAGGTTGGCATGTATACACTATGAAAA
CGGCAAGTCCACATCACCCAGGAGGACTTTGAGATGGCAGTAGTCAAGCTCATGCAGAAGGATAGTGAGAAAAACATGTC
CATCAAGAAACTTTTGAAG

Alignment

ORF - retro_itri_1046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALDGPEQMELEEGKAGS-GLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR-EELQLLQE
          MALDGP..MELEEGKAGS.GL.QYYLSKIEELQLIVNDKSQNL.RLQ.QRN.LNAKV.LL..E.LQLLQE
Retrocopy MALDGPGKMELEEGKAGSSGLHQYYLSKIEELQLIVNDKSQNLQRLQVQRNKLNAKVHLLQ<EKLQLLQE

Parental  QGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDI-NDVTPNCRVA-LRNDSYTLHKILPNKVDPLVS
          QGS.V.EVVRAM.KKKVLVKVHP.GKFVVDVDKNI.I..DVT.NCRVA.LRNDSYTLHKILPNKVDPLVS
Retrocopy QGSHVEEVVRAMVKKKVLVKVHPKGKFVVDVDKNINI<HDVTLNCRVA>LRNDSYTLHKILPNKVDPLVS

Parental  LMMVEKVPDSTY-EMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAH
          LMMVEKVPDSTY..MIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLA.AVAH
Retrocopy LMMVEKVPDSTY<QMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLAQAVAH

Parental  HTDCTFIRVSGSELVQKFIGEGARMVRELFVMAREHAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLE
          .TDCTFIRVS.SELVQKFIGEGA.M.RELFVMA..HAPSIIFMDEIDSIGSS.LEGGSGGDSE.QRTMLE
Retrocopy PTDCTFIRVSSSELVQKFIGEGAKMGRELFVMAQKHAPSIIFMDEIDSIGSSWLEGGSGGDSEMQRTMLE

Parental  LLNQLDGFEATKNIKVIMATNRIDILDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLR
          LLNQLDGFEATKNIK..MATNRIDILDSALL.PGRIDRKIEFPPPNEEA.LDILKIHS.KMNL..GINL.
Retrocopy LLNQLDGFEATKNIKIVMATNRIDILDSALLHPGRIDRKIEFPPPNEEAPLDILKIHSWKMNLIQGINLI

Parental  KIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK
          KIAELMPGASGAEVKGVC.E.GMY.L..R.VH.TQEDFEMAV.K.MQKDSEKNMSIKKL.K
Retrocopy KIAELMPGASGAEVKGVCIEVGMYTL*KRQVHITQEDFEMAVVKLMQKDSEKNMSIKKLLK

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_1046 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1046 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046 ,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,