RetrogeneDB ID: retro_itri_1621

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393578.1:1178423..1178983(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSSTOG00000000098
• Aliases: None
• Description: NGFI-A binding protein 1 (EGR1 binding protein 1) [Source:HGNC Symbol;Acc:7626]

Sequence

>retro_itri_1621
GGGAAGTCAGATGTGATGGGAGTTTAGCACAACAGACTCTGGCAAGGCCACCATGCTACTGAGAGGGAACACAGTCTGAC
CCCAGCAGACCGTGGCTCTCCAGCTTTCTCCAAGGAAAGCAGTGAGGCACTGGATGCTGCTGCTGCCTTCTCTGTGGCTG
AGTGTGTGGAGCGAATGGCCCCCACACTGACAAAAAGTGACTTGAATGAAGGGAAAGAGCTGCTAAAAACCAACAAGAAG
TTGGCCAAAATTGTCACGTTTTTGAAATGAGTAATGATGATCCACAAAAAGAGGAGGAAATTCGAAAATACAGTGCAATG
TATGGCAGATTTGATTCAAATAAAAAGGATGGGAAACATCTCACACTTCATGAGCTCACTGTTAACGAAGCAGCTGCCCA
ATTCTATGTGAAAGATAATGCCCAGCTTACAAGAAGAGATGAACTTTTTGCTCTGGCTAGGCATATTTCTCGAGAAGTCA
CTTATGAATATACTTACAGATACATCAAGTCAACATGTGGTGAAAGAGATGAATTATCCCTAAAGAGAATTAAAATAGAG

Alignment

ORF - retro_itri_1621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.72 %
• Parental protein coverage: 56.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSLALQSVGESRLWQGHHATESEHSLSPADLGSPASPKESSEALDAAAALSVAECVERMAHTLPKSDLNE
          G......V...RLWQGHHATE.EHSL.PAD.GSPA..KESSEALDAAAA.SVAECVERMA.TL.KSDLNE
Retrocopy GKSDVMGV*HNRLWQGHHATEREHSLTPADRGSPAFSKESSEALDAAAAFSVAECVERMAPTLTKSDLNE

Parental  VKELL-KNNKKLAKMIGHIFEMSDDDPHKEEEIRKYSAIYGRFDSKRKDGKHLTLHELTVNEAAAQLCVK
          .KELL.KN.........H.FEMS.DDP.KEEEIRKYSA.YGRFDS..KDGKHLTLHELTVNEAAAQ..VK
Retrocopy GKELL<KNQQEVGQNC-HVFEMSNDDPQKEEEIRKYSAMYGRFDSNKKDGKHLTLHELTVNEAAAQFYVK

Parental  DNALLTRRDELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIKVE
          DNA.LTRRDELFALAR.ISREVTY.YTYR..KS.CGERDELS.KRIK.E
Retrocopy DNAQLTRRDELFALARHISREVTYEYTYRYIKSTCGERDELSLKRIKIE

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_1621 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1621 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621 ,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626,