RetrogeneDB ID: retro_itri_931

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393345.1:8350560..8351078(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYCP3
• Ensembl ID: ENSSTOG00000001853
• Aliases: None
• Description: synaptonemal complex protein 3 [Source:HGNC Symbol;Acc:18130]

Sequence

>retro_itri_931
CAAGACATGGAGAATGAACTACAGAATATGTTGGCAAGTTTCAAGGGGACATCGAGAAGCTTCTTCAGGCAAAGAGAAAA
AATGTTCGAAATGAGTATCAGTGCTTCTGTCAAAACCATTCAGCAGAAAATTGAGCATGTTCTGAAAATCCATCGTGAGC
AAAAGGAGGAGCTTTATGAAGAATAATGTCATCAGTTTGCGACTATGATTCAGATGTGGAACCCAGATATGAAGAAAGTC
AAGGAACGAGGAGGAAAACTAGGTAGTATATTTCAACAACAACGAAAGGCTTTCCAACAATCTCAACTTGTTCAGAACCA
GAAAATGAAAACCTTTAGAAAGTTATGTTACCAATTATTGGAGATCTGCTGGACCTAGAGGAGAATCATGGAAAAGTTCT
TGCTGGTGAACAAAGTGAATTTAGGAAACAGATGGCCATCTTGCAAACAAAACTTATGATGGAATCTTGGCAGGAGGAGA
AGCCCAGTGCTCAAAAATCTCTGCTATCCCTGTTATTC

Alignment

ORF - retro_itri_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.57 %
• Parental protein coverage: 72.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDMGGEVQNMLE-KFGADINKALLAKRKRL-EMYTKASFKTSNQKIEHVWKTQQEQRQKLNQEYSQQFMN
          .DM..E.QNML..KF..DI.K.L.AKRK...EM...AS.KT..QKIEHV.K...EQ...L..E...QF..
Retrocopy QDMENELQNMLA<KFQGDIEKLLQAKRKNV>EMSISASVKTIQQKIEHVLKIHREQKEELYEE*CHQFAT

Parental  LFQQWDIDLQKAEEQEEKLANMFRQQQKVFQQSRIVQNQRLKTIRQLYEQFVK-SLEDLEKNHDNLLTGT
          ..Q.W..D..K..E...KL...F.QQ.K.FQQS..VQNQ..KT.R.L..Q.....L.DLE.NH...L.G.
Retrocopy MIQMWNPDMKKVKERGGKLGSIFQQQRKAFQQSQLVQNQKMKTFRKLCYQLLE<DLLDLEENHGKVLAGE

Parental  QSELKKEMAMLQKKIMMETQQQEMASVRKSLQSMLF
          QSE..K.MA.LQ.K.MME..Q.E..S..KSL.S.LF
Retrocopy QSEFRKQMAILQTKLMMESWQEEKPSAQKSLLSLLF

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_931 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_931 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402, retro_dnov_420,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Mus musculus	ENSMUSG00000067764	1 retrocopy	retro_mmus_1085,
Mus musculus	ENSMUSG00000072479	1 retrocopy	retro_mmus_1782,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Rattus norvegicus	ENSRNOG00000017224	1 retrocopy	retro_rnor_1728,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931 ,