RetrogeneDB ID: retro_itri_1336

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393445.1:980499..981236(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX19A
• Ensembl ID: ENSSTOG00000006938
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A [Source:HGNC Symbol;Acc:25628]

Sequence

>retro_itri_1336
ATGGACACAAAAAGAATCAAGATATTTGTTCTGGATGAGGCTGACATGATGATAGCCACTCAGGGCCACCAAGATCAGAG
CATCCATATCCAGAGGATGCCACCCAAGAACTGCCAGATGTTGCTTTTCTCTGCCACGTTTGAAGTCGCTGTGTTGAAAT
TTGCTCAGAAAGTAGTTCTGAGCAACATTATCAAAGTAAAGTGTGAGTAGGAGATTTTGGACATCATCAAGCAATACTAT
GACCTGTGCAGTAACAGAGATGAGAAGTTCTAGACCTTGTGCAACCTGTATGGGGCCATCACCATCGCTCAAGCCATGAT
CTTCTGCCATATCTGCAAAATAGCTAGTTGACTGACAGCAGAGTTCTCAAAAGAAGGCCCCCAAGAGGCCCTGGTGAGTG
GAGAAATAATGGTGGAGCAGAGAACTGCTGTTATTGAGTGCTTCTGAGAGGGTAAAGAGAAGGTTCTGGTGACCCCCAAG
GTGTGAGCTTGTGGTATCAATGTTGACCAAGTGTCTGTTGTTATCAACTTCAATTTTCCTGTGGACAAGGATGGGAACCC
AGACAACATGATCTACTTGTACTGGATCGGGTGTACTGGTCACTTTGGCAAGAGGGGACTGACTGTGAACATTATCAAGC
ACAGCATGAACATCCTGAATAGAATCCAGGAGCATTTTAATAAGAGATAGAAAAATTAGACATGGATGATTCAGATGAGA
TTGAGAAAATAGCCAGT

Alignment

ORF - retro_itri_1336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.0 %
• Parental protein coverage: 51.98 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDPKRIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNIIKLKRE
          .D.KRIK.FVLDEAD.MIATQGHQDQSI.IQRM.P.NCQMLLFSATFE..V.KFAQKVV...NIIK.K.E
Retrocopy MDTKRIKIFVLDEADMMIATQGHQDQSIHIQRMPPKNCQMLLFSATFEVAVLKFAQKVVLS-NIIKVKCE

Parental  EETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVE
          .E.LD.IKQYY.LC.NRDEKF..LCNLYGAITIAQAMIFCH..K.AS.L.AE.SKEG.Q.AL.SGE.MVE
Retrocopy *EILDIIKQYYDLCSNRDEKF*TLCNLYGAITIAQAMIFCHICKIAS*LTAEFSKEGPQEALVSGEIMVE

Parental  QRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAV
          QR.AVIE.F.EGKEKVLVT..V.A.GI.V.QVSVVINF..PVDKDGNPDN..YL..IG.TG.FGKRGL.V
Retrocopy QRTAVIECF*EGKEKVLVTPKV*ACGINVDQVSVVINFNFPVDKDGNPDNMIYLYWIGCTGHFGKRGLTV

Parental  NMVDSKHSMNILNRIQEHFNKK-IERLDTDDLDEIEKIAN
          N....KHSMNILNRIQEHFNK..IE.LD.DD.DEIEKIA.
Retrocopy NII--KHSMNILNRIQEHFNKR<IEKLDMDDSDEIEKIAS

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_1336 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1336 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010419	1 retrocopy	retro_etel_696,
Ictidomys tridecemlineatus	ENSSTOG00000006938	1 retrocopy	retro_itri_1336 ,
Ictidomys tridecemlineatus	ENSSTOG00000025733	1 retrocopy	retro_itri_1877,