RetrogeneDB ID: retro_itri_1320

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393440.1:1692590..1693931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B4
• Ensembl ID: ENSSTOG00000013683
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 4 [Source:HGNC Symbol;Acc:5213]

Sequence

>retro_itri_1320
GAATCAGTTGCAGGTATGATTGAAGTTTTACATAAAATAGATGCAGAAGGAGGAGTTTCAATAAATCATACCAGTCATGC
AACATCTACAGCTACTTCAGGATTTGCTGGAGCTATTGGCTATAAACTCCCTTCATTTTCTTCTGCTTACATGGAAATGG
AAACAATTATGTATGCTCTTGGAGTGGGAGCATCTGTCAAAGATCCAAAGGATTTGAAATTTGTTTATGAAGGAAGTTCT
TATTTCTCCTGTTTGCCTACCTTTGGAGTTATCATAGCTCAGAAATCTATGATGGGTGGAGGATTAGCAGATATTCCTGG
GCTTTCAATCAACTTTGCACAGGTTCTTCACGGGGAGCAATACTTGGAGTTATATAAACCTCTTCCTAGATCAGGAAAAT
TAAAATGTGAAGCAGTTGTTGCTGATGTCCTAGATAAAGGATCTGGCGCAGTAATTCTTATGGATGTCTATTCTTATTCT
GGGAAGGAACTTATATACTATAATCAGTTCTCTCTCTTTCTGGTTGGCTCTGGAGGCTTTGGAGGAAAACGGACATCAGA
AAAACTCAAGGTAGCTCTCGACGTACCTAGTAGATCTCCGGATGCTGTACTTAGAGATACCACCTCACTTAATCAGGCTG
CTTTGTACCGCCTCAGTGGAGACTGGAATCCCTTACACATTGACCCTAACTTTGCTAGCCTTGCAGGCTTTGAGAAGCCC
ATATTACACGGATTATGTACCTTTGGATTTTCTGCCAGGCATGTTTTACAGCAGTTTGCGGATAATGATGTCTCAAGGTT
CAAGGCAATTAAGACTCGTTTTGCAAAACCAGTATATCCGGGACAAACTCTACAAACTGAAATGTGGAAGGAAGGAAACA
GGATTCATTTTCAAACTAAGGTCCAAGAAACTGGAGACATTGTCATTTCAAATGCATATGTGGATCTTGTGCCCAAATTA
GATATTTCAGCTAAGATACCCTCTGAGGGTGGCGAGCTTCAAAGTACTCTTGTGTTTGAGGAAATAGGTCGGCGCCTTAA
GGAAGTTGGGCGTGAGGTGGTAAAGAAAGTAAAAGCTGTGTTTGAGTGGCATATCACTAAAGGTGGAGACATTGCAGCTA
AGTGGACAATTGACCTGAAAAATGAATCTGGAAAAGTATACAAAGGCCCTGCAAAAGGCTGTGCTGATACGACTATCATA
ATTTCAGATGATGATTTCATGCAGGTAGTTCTGGGCAAGCTTGACCCTCAGAAGGCATTCTTTAGTGGCCGACTGAAGGC
CAGAGGGAACATCATGCTGAGCCAGAAACTCCAGATGATTCTTAAAGACTATGCCAAGCTC

Alignment

ORF - retro_itri_1320 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.88 %
• Parental protein coverage: 60.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESVAGMIEVLHKIDAEGGVSINHTSHATSTATSGFAGAIGYKLPSFSSAYTEMETIMYALGVGASVKDPK
          ESVAGMIEVLHKIDAEGGVSINHTSHATSTATSGFAGAIGYKLPSFSSAY.EMETIMYALGVGASVKDPK
Retrocopy ESVAGMIEVLHKIDAEGGVSINHTSHATSTATSGFAGAIGYKLPSFSSAYMEMETIMYALGVGASVKDPK

Parental  DLKFVYEGSSDFSCLPTFGVIIAQKSMMGGGLAEIPGLSINFAQVLHGEQYLELYKPLPRSGKLKCEAVV
          DLKFVYEGSS.FSCLPTFGVIIAQKSMMGGGLA.IPGLSINFAQVLHGEQYLELYKPLPRSGKLKCEAVV
Retrocopy DLKFVYEGSSYFSCLPTFGVIIAQKSMMGGGLADIPGLSINFAQVLHGEQYLELYKPLPRSGKLKCEAVV

Parental  ADVLDKGSGAVILMDVYSYSGKELICYNQFSLFLVGSGGFGGKRTSEKLKVALDVPSRSPDAVLRDTTSL
          ADVLDKGSGAVILMDVYSYSGKELI.YNQFSLFLVGSGGFGGKRTSEKLKVALDVPSRSPDAVLRDTTSL
Retrocopy ADVLDKGSGAVILMDVYSYSGKELIYYNQFSLFLVGSGGFGGKRTSEKLKVALDVPSRSPDAVLRDTTSL

Parental  NQAALYRLSGDWNPLHIDPNFASLAGFEKPILHGLCTFGFSARHVLRQFADNDVSRFKAIKTRFAKPVYP
          NQAALYRLSGDWNPLHIDPNFASLAGFEKPILHGLCTFGFSARHVL.QFADNDVSRFKAIKTRFAKPVYP
Retrocopy NQAALYRLSGDWNPLHIDPNFASLAGFEKPILHGLCTFGFSARHVLQQFADNDVSRFKAIKTRFAKPVYP

Parental  GQTLQTEMWKEGNRIHFQTKVQETGDIVISNAYVDLVPKLDISAKIPSEGGELQSTLVFEEIGRRLKEVG
          GQTLQTEMWKEGNRIHFQTKVQETGDIVISNAYVDLVPKLDISAKIPSEGGELQSTLVFEEIGRRLKEVG
Retrocopy GQTLQTEMWKEGNRIHFQTKVQETGDIVISNAYVDLVPKLDISAKIPSEGGELQSTLVFEEIGRRLKEVG

Parental  REVVKKVKAVFEWHITKGGDIAAKWTIDLKNESGKVYKGPAKGCADTTIIISDDDFMQVVLGKLDPQKAF
          REVVKKVKAVFEWHITKGGDIAAKWTIDLKNESGKVYKGPAKGCADTTIIISDDDFMQVVLGKLDPQKAF
Retrocopy REVVKKVKAVFEWHITKGGDIAAKWTIDLKNESGKVYKGPAKGCADTTIIISDDDFMQVVLGKLDPQKAF

Parental  FSGRLKARGNIMLSQKLQMILKDYAKL
          FSGRLKARGNIMLSQKLQMILKDYAKL
Retrocopy FSGRLKARGNIMLSQKLQMILKDYAKL

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_1320 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1320 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013683	1 retrocopy	retro_itri_1320 ,
Ictidomys tridecemlineatus	ENSSTOG00000028886	1 retrocopy	retro_itri_245,