RetrogeneDB ID: retro_itri_1079

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393370.1:258886..259231(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLVRB
• Ensembl ID: ENSSTOG00000002958
• Aliases: None
• Description: biliverdin reductase B (flavin reductase (NADPH)) [Source:HGNC Symbol;Acc:1063]

Sequence

>retro_itri_1079
GTGGGTGATCGTCAGCAGCCAGCTGACTTGGTGGGAATGTACCCAAGCAAGGTGCTGTTGATGTGCTGAACACTGGCCCT
GACTTTAGTCCTGCTACAGTGATGTCTCAGAGCCCTGGAACATTGTGGCTGCAATAAATGTCCACAGAGTACGCAAGGTT
TTGGCCTGATTCTCCCTCTTCCTTCTATGGGACCCAGCCAACATGCTCCTGCACTGCAGGATGTAAACAATAACCATATC
TGGATGCACAAAGTATTTCAGGAACAGGTCCTGAAGTACATGTCCATGATGCTGCCACACATAGGACACCAGCCACTAAC
TGGGACTTACTTGGTGACCCTGGAT

Alignment

ORF - retro_itri_1079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 63.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGDVRQAADV-DKTVAGQDAVIVLLGTGTDLSPTTVMSEGAR-NIVAAMKAHGVDKVVACTSAFLLWDPA
          VGD..Q.AD.....V..Q.AV.VL..TG.D.SP.TVMS.....NIVAA...H.V.KV.A..S.FLLWDPA
Retrocopy VGDRQQPADL<GGNVPKQGAVDVL-NTGPDFSPATVMSQSPG<NIVAAINVHRVRKVLA*FSLFLLWDPA

Parental  KV-PPRLQDVTDDHIRMHKVLQESGLKYVAVMPPHIGDQPLTGAYTVTLD
          ....P.LQDV...HI.MHKV.QE..LKY...M.PHIG.QPLTG.Y.VTLD
Retrocopy NM<APALQDVNNNHIWMHKVFQEQVLKYMSMMLPHIGHQPLTGTYLVTLD

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_1079 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1079 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010508	2 retrocopies	retro_btau_289, retro_btau_718,
Rattus norvegicus	ENSRNOG00000024410	1 retrocopy	retro_rnor_1341,
Ictidomys tridecemlineatus	ENSSTOG00000002958	1 retrocopy	retro_itri_1079 ,
Tupaia belangeri	ENSTBEG00000015357	2 retrocopies	retro_tbel_2799, retro_tbel_4031,