RetrogeneDB ID: retro_itri_1665

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393619.1:769497..770084(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD7
• Ensembl ID: ENSSTOG00000013123
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 [Source:HGNC Symbol;Acc:9565]

Sequence

>retro_itri_1665
AGAATCATTGTCTGGTACCACCCAGGCCCTAAACAACTATGTAAGAATGACATTGCCATCAATTAACTCATGAAAACATA
CTGCCCTAACTCAGTATTGGTCATTATCATGCAAAGCCAGAAAACCTGGGGCTGCCCACAGAAACATGTATTTCAGGCGA
AGAAGTTCATGATGATGGAACTCCAACCTTGAAAACATTTGAGCATGTGACTGGGAAAATTGGAGCAGAAGAAGCTAAGG
AAGTTGGGGTTGAACACTTATTGTGAAACATCAAGGACGGTACAGTGGGCAGTCTTTCCAAGTGGATCACAAATCAGGGC
CATGGTTTGAAGGGACTGAACTCCAAGTTTCTAGATATCGGGAGCTACCTGGAAAAAGTAGCCACAGGCAAGCTGCCCAT
CAACCACCAGATCATCTACCAGCTGCAGGACGTCTTCAACCTGCTGCCTGATGTCAGCCTGCAGGAGTTTGTCAAGGCCT
TTTACCTGAAGACTAATGACCAGATGATGATGGTGTACTTGGCCTCGCTGACCCGCTCCGTAGTTGCCCTGCACAACCTC
ATTAACAACAAGATTGCCAACCAGGAT

Alignment

ORF - retro_itri_1665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 60.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIVGWYHTGPK-LHKNDIAINELMKRYCPNSVLVII-DVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEH
          RI..WYH.GPK.L.KNDIAIN.LMK.YCPNSVLVII...KP..LGLPTE..IS.EEVHDDGTPT.KTFEH
Retrocopy RIIVWYHPGPKQLCKNDIAIN*LMKTYCPNSVLVII<HAKPENLGLPTETCISGEEVHDDGTPTLKTFEH

Parental  VTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLLDIRSYLEKVATGKLPINHQII
          VT..IGAEEA.EVGVEHLL..IKD.TVG.LS..ITNQ.HGLKGLNSK.LDI.SYLEKVATGKLPINHQII
Retrocopy VTGKIGAEEAKEVGVEHLL*NIKDGTVGSLSKWITNQGHGLKGLNSKFLDIGSYLEKVATGKLPINHQII

Parental  YQLQDVFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIANRD
          YQLQDVFNLLPDVSLQEFVKAFYLKTNDQM..VYLASL.RSVVALHNLINNKIAN.D
Retrocopy YQLQDVFNLLPDVSLQEFVKAFYLKTNDQMMMVYLASLTRSVVALHNLINNKIANQD

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_1665 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1665 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Ictidomys tridecemlineatus	ENSSTOG00000013123	1 retrocopy	retro_itri_1665 ,