RetrogeneDB ID: retro_itri_414

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:4401659..4402359(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL1
• Ensembl ID: ENSSTOG00000000075
• Aliases: None
• Description: thioredoxin-like 1 [Source:HGNC Symbol;Acc:12436]

Sequence

>retro_itri_414
ATGAGTAATAAATATCCACAGGCTGTTTTCTTGGAAGTAGATGTACATCAGTGTCAGGGAACTGCTGCCACAAACAATAT
ATCAGCAACACCTACGGTTTTGTTTTTTCGAAACAAAGTGAGGATGGATCAATATCAAGGAGCAGATGCTGTTGGATTAG
AAGAAAAAAATCAAGCAACACTTAGAAAGTGACCTTGGAAGCAATGAGGACACAGTTATTCCAAAAGGTTATATGGATTA
AATGCCTTTTATTAACAAGGCTGGTTGTGAATGTTTCAATCAAAGCGGTGAACATGGTTTTGACAACTGTTTACGAAAAG
ACATGGCCTTCTTGGAATCTGACTGTGATGAACAGCTACTTATTACTGTGGCATTCAATCAACCTGTTAAGCTTTATTCC
ATGAAATTTCAAGGGCCAGATAATGGTCAGGGTCCTAAATATGCAAAAATTTTTATCAACCTACCCTGATCTATGGATTT
TGAAGAGACAGAAAGAAGTGAACCAACTCAAGCTTTGGAACTGACAGAGGATGATATCAAAGAAGATGGCATTGTTCCAC
TTCTTTATGTTAAGTTTCAGAGTGTTAACAGTGTAACTATATTTGTTCAGTCTAATCAGGGTGAAGAAGAAACAACAAGA
ATTTCCTATTTTACTTTTATTGGTACTCCAGTCCAGGCAACAAATATGAATGACTTCAAA

Alignment

ORF - retro_itri_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 95.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSNKYPQAVFLEVDVHQCQGTAATNNISATPTFLFFRNKVRIDQYQGADAVGLEEK-IKQHLENDPGSNE
          MSNKYPQAVFLEVDVHQCQGTAATNNISATPT.LFFRNKVR.DQYQGADAVGLEEK.IKQHLE.D.GSNE
Retrocopy MSNKYPQAVFLEVDVHQCQGTAATNNISATPTVLFFRNKVRMDQYQGADAVGLEEK>IKQHLESDLGSNE

Parental  DTDIPKGYMDLMPFINKAGCECLNESDEHGFDNCLRKDMTFLESDCDEQLLITVAFNQPVKLYSMKFQGP
          DT.IPKGYMD.MPFINKAGCEC.N.S.EHGFDNCLRKDM.FLESDCDEQLLITVAFNQPVKLYSMKFQGP
Retrocopy DTVIPKGYMD*MPFINKAGCECFNQSGEHGFDNCLRKDMAFLESDCDEQLLITVAFNQPVKLYSMKFQGP

Parental  DNGQGPKYVKIFINLPRSMDFEEAERSEPTQALELTEDDIKEDGIVPLRYVKFQNVNSVTIFVQSNQGEE
          DNGQGPKY.KIFINLP.SMDFEE.ERSEPTQALELTEDDIKEDGIVPL.YVKFQ.VNSVTIFVQSNQGEE
Retrocopy DNGQGPKYAKIFINLP*SMDFEETERSEPTQALELTEDDIKEDGIVPLLYVKFQSVNSVTIFVQSNQGEE

Parental  ETTRISYFTFIGTPVQATNMNDFK
          ETTRISYFTFIGTPVQATNMNDFK
Retrocopy ETTRISYFTFIGTPVQATNMNDFK

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_414 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_414 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000137	1 retrocopy	retro_cfam_875,
Choloepus hoffmanni	ENSCHOG00000010262	1 retrocopy	retro_chof_1723,
Ictidomys tridecemlineatus	ENSSTOG00000000075	2 retrocopies	retro_itri_302, retro_itri_414 ,
Ictidomys tridecemlineatus	ENSSTOG00000020668	4 retrocopies	retro_itri_6, retro_itri_714, retro_itri_823, retro_itri_884,
Tupaia belangeri	ENSTBEG00000017328	2 retrocopies	retro_tbel_1981, retro_tbel_911,
Tursiops truncatus	ENSTTRG00000001161	1 retrocopy	retro_ttru_1154,