RetrogeneDB ID: retro_pabe_1695

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19_random:6770339..6770947(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IST1
• Ensembl ID: ENSPPYG00000007522
• Aliases: None
• Description: IST1 homolog [Source:RefSeq peptide;Acc:NP_001126550]

Sequence

>retro_pabe_1695
ATGCTGGGCTCTGGATTTAAAGCTGAGCGTTTAAGAGTGAATTTGAGATTAGTCATAAATCGCCTTAAACTATTGGAGAA
AAAAAAACGGAACTGGCCCAGAAAGCAAGGAAGGAGATTGCTGACTATCTGGCTGCTGGGAAAGATGAACGAGCTTGGAT
CCGTGTGGAGCACATTATCCGGGAAGACTACCTCGTGGAGGCCATGGAGATCCTGGAGCTGTACTGTGATCTGCTGCTGG
CTCGGTTTGGCCTTATCCAGTCTATGAAGGAACTAGATTCTGGTCTGGCTTAATCTGTGTCTACATTGATCTGGGCTGCT
CCTCGACTCCAGTCAGAAGTGGCTGAGTTGAAAATAGTTGCTGATCAGCTCTGTGCCAAGTATAGCAAGGAATATGGCAA
GCTGTGTAGGACCAACCAGATTGGAACTGTGAATGACAGGCTAATGCACAAGCTGAGTGTGGAAGCCCCATCCAAAATCC
TGGTGGAGAGATACCTGATTGAAATTGCGAAGAATTACAATGTACCCTATGAACCTGACTCTGTGGTCATGGCAGAAGCT
TCTTCTGGGGTAGAGACAGAGCTTATTGATGTTGAATTCACAGATGAT

Alignment

ORF - retro_pabe_1695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 55.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLGSGFKAERLRVNLRLVINRLKLLEKKKT-ELAQKARKEIADYLAAGKDERARIRVEHIIREDYLVEAM
          MLGSGFKAERLRVNLRLVINRLKLLE.....ELAQKARKEIADYLAAGKDERA.IRVEHIIREDYLVEAM
Retrocopy MLGSGFKAERLRVNLRLVINRLKLLEXXXR<ELAQKARKEIADYLAAGKDERAWIRVEHIIREDYLVEAM

Parental  EILELYCDLLLARFGLIQSMKELDSGLAESVSTLIWAAPRLQSEVAELKIVADQLCAKYSKEYGKLCRTN
          EILELYCDLLLARFGLIQSMKELDSGLA.SVSTLIWAAPRLQSEVAELKIVADQLCAKYSKEYGKLCRTN
Retrocopy EILELYCDLLLARFGLIQSMKELDSGLA*SVSTLIWAAPRLQSEVAELKIVADQLCAKYSKEYGKLCRTN

Parental  QIGTVNDRLMHKLSVEAPPKILVERYLIEIAKNYNVPYEPDSVVMAEAPPGVETDLIDVGFTDD
          QIGTVNDRLMHKLSVEAP.KILVERYLIEIAKNYNVPYEPDSVVMAEA..GVET.LIDV.FTDD
Retrocopy QIGTVNDRLMHKLSVEAPSKILVERYLIEIAKNYNVPYEPDSVVMAEASSGVETELIDVEFTDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.33 RPM	35.83 RPM
SRP007412_cerebellum	0.36 RPM	43.78 RPM
SRP007412_heart	0.18 RPM	18.60 RPM
SRP007412_kidney	0.36 RPM	39.21 RPM
SRP007412_liver	0.18 RPM	24.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1695 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015051	1 retrocopy	retro_cjac_1906,
Dipodomys ordii	ENSDORG00000002409	1 retrocopy	retro_dord_398,
Gorilla gorilla	ENSGGOG00000001863	1 retrocopy	retro_ggor_1446,
Mustela putorius furo	ENSMPUG00000007857	1 retrocopy	retro_mputfur_415,
Pongo abelii	ENSPPYG00000007522	1 retrocopy	retro_pabe_1695 ,
Sus scrofa	ENSSSCG00000002743	1 retrocopy	retro_sscr_349,