RetrogeneDB ID: retro_itri_1877

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394342.1:42631..43394(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX19B
• Ensembl ID: ENSSTOG00000025733
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B [Source:HGNC Symbol;Acc:2742]

Sequence

>retro_itri_1877
TCCAAGTTCAGGTTCATTGACTCCAGAAGGATCAAGGTGTTTGTTCTGAATGAGGCTGACGTGATGATAGCCACTCAGGG
CCACCAAGATCAGAGCATCCCTATCCAGAGGCTGCTACCCAAGAACTGCCAGATGTTGCTTTTCTCTGCCACTTTTGAAG
ACTCTGTGTGGAAGTTTGCCCAGAAAGTGGTCCCAGATCCCTAATATTATCAAACTGAAGCATGAGGAGGAGACATTGGA
TACCATCAAGCAGTACTATATCCTGTGCAATAATAGAGATGAGAAATTCCAGGCCTTCTGCAACCTGTATGGGGCCATCA
CCATCGCACAAGCCATAATTTTCTGCCATATCCGCAAAACAGCTAGTTGGTTTGCAGCAGAGCTCTCAAAAGAAGGCCAC
CAGGTGGCTCTGCTGAGTGGAGAAATGATGGTGGAGCAGAGGGCTACTGTGATGGAGCGCTTCTGAGAGGGCAAAGAGAA
GGTTCTGGTGACCACCAACATGTGTGCTCGTGGTATGGATGTTGAACAAGTGTCTGTCGTCATCAACTTCGATTTTTCTG
TGGACAAGGATGGGAACCCAGACCACCAGACCTACCTGCACCAGACTGGACACACTGGTCGCTTTGGCAAGAGAGGCCTG
GCCGTGAACATGGTTGACAGCAAGCACAGCATGAGCATCCTGAACAGAATCCAGGAGCATTTTAATAGGAAGATAGGAAA
ATTGAATACAGATGATTTGGACGAGATTGAGAAAATAGCCAAC

Alignment

ORF - retro_itri_1877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.63 %
• Parental protein coverage: 53.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKLRFIDPRRIKVFVLDEADVMIATQGHQDQSIRIQRMLPKNCQMLLFSATFEDSVWKFAQKVVPDP-NI
          SK.RFID.RRIKVFVL.EADVMIATQGHQDQSI.IQR.LPKNCQMLLFSATFEDSVWKFAQKVVPDP.NI
Retrocopy SKFRFIDSRRIKVFVLNEADVMIATQGHQDQSIPIQRLLPKNCQMLLFSATFEDSVWKFAQKVVPDP>NI

Parental  IKLKREEETLDTIKQYYVLCNNRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLS
          IKLK.EEETLDTIKQYY.LCNNRDEKFQA.CNLYGAITIAQA.IFCH.RKTASW.AAELSKEGHQVALLS
Retrocopy IKLKHEEETLDTIKQYYILCNNRDEKFQAFCNLYGAITIAQAIIFCHIRKTASWFAAELSKEGHQVALLS

Parental  GEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFG
          GEMMVEQRA.V.ERF.EGKEKVLVTTN.CARG.DVEQVSVVINFD..VDKDGNPD..TYLH..G.TGRFG
Retrocopy GEMMVEQRATVMERF*EGKEKVLVTTNMCARGMDVEQVSVVINFDFSVDKDGNPDHQTYLHQTGHTGRFG

Parental  KRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTDDLDEIEKIAN
          KRGLAVNMVDSKHSM.ILNRIQEHFN.KI..L.TDDLDEIEKIAN
Retrocopy KRGLAVNMVDSKHSMSILNRIQEHFNRKIGKLNTDDLDEIEKIAN

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_1877 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1877 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010216	1 retrocopy	retro_chof_106,
Ictidomys tridecemlineatus	ENSSTOG00000006938	1 retrocopy	retro_itri_1336,
Ictidomys tridecemlineatus	ENSSTOG00000025733	1 retrocopy	retro_itri_1877 ,
Tupaia belangeri	ENSTBEG00000009816	1 retrocopy	retro_tbel_3669,