RetrogeneDB ID: retro_pabe_2386

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:176181934..176182488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC31A1
• Ensembl ID: ENSPPYG00000019514
• Aliases: None
• Description: high affinity copper uptake protein 1 [Source:RefSeq peptide;Acc:NP_001125663]

Sequence

>retro_pabe_2386
ATGGATCATTCCCATGATACAGGGATGAGCTATATGGACTCCAACAGTACCATGCAACCTCCTCGCCATCACCCAACCAC
TTCAGCCTCACACTCCCGTGGTGGAGGAGACAGCAACATGATGATGATGATGCCTATGGCCTTCTACTTTGGCTTTAAGA
ACGTGGAACTACTGTTTTCCGGTTTGGTGATCAATACAGCTGGAGAAATGGCTGGAGCTTTTGTGGCAGTGTTTATACTA
GCAGTGTTCTATGAAGGACTCAAGATAGCCCGAGAGAGCCTGCTGTGTAAGTCACAAGTCAGCATTTGCTACAATTCCAT
GCCTGTCCCAGGACCAAATGGAACCATCCTTATGTAAACACACAAAACTGTTGGGCAGCAGATGCTGAGCTTTCCTCACC
TCCTGCAAACAGTGCTGCACATCATCCAGTGGTCATAAGCTACTTCTTCATGCTCATCTTCATGACCTACAATGGGTACC
TCTGCATTGCAGTAGCAGCAGGGGCCGGTACAGGATACTTCCTCTTCAGCTGGAAGAAGGCAGTGGTAGTGGAC

Alignment

ORF - retro_pabe_2386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.94 %
• Parental protein coverage: 96.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDHSHHMGMSYMDSNSTMQPSHHHPTTSASHSHGGGDSSMMMM-PMTFYFGFKNVELLFSGLVINTAGEM
          MDHSH..GMSYMDSNSTMQP..HHPTTSASHS.GGGDS.MMMM.PM.FYFGFKNVELLFSGLVINTAGEM
Retrocopy MDHSHDTGMSYMDSNSTMQPPRHHPTTSASHSRGGGDSNMMMMMPMAFYFGFKNVELLFSGLVINTAGEM

Parental  AGAFVAVFLLAMFYEGLKIARESLLRKSQVSIRYNSMPVPGPNGTILMETHKTVGQQMLSFPHLLQTVLH
          AGAFVAVF.LA.FYEGLKIARESLL.KSQVSI.YNSMPVPGPNGTILM.THKTVGQQMLSFPHLLQTVLH
Retrocopy AGAFVAVFILAVFYEGLKIARESLLCKSQVSICYNSMPVPGPNGTILM*THKTVGQQMLSFPHLLQTVLH

Parental  IIQ-VVISYFLMLIFMTYNGYLCIAVAAGAGTGYFLFSWKKAVVVD
          IIQ.VVISYF.MLIFMTYNGYLCIAVAAGAGTGYFLFSWKKAVVVD
Retrocopy IIQ<VVISYFFMLIFMTYNGYLCIAVAAGAGTGYFLFSWKKAVVVD

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	0.00 RPM	13.82 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.03 RPM	8.43 RPM
SRP007412_kidney	0.10 RPM	36.40 RPM
SRP007412_liver	0.28 RPM	58.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2386 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2386 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011908	5 retrocopies	retro_chof_1186, retro_chof_1646, retro_chof_1661, retro_chof_644, retro_chof_776,
Felis catus	ENSFCAG00000005512	1 retrocopy	retro_fcat_425,
Macropus eugenii	ENSMEUG00000015425	2 retrocopies	retro_meug_1049, retro_meug_1533,
Microcebus murinus	ENSMICG00000015008	2 retrocopies	retro_mmur_1465, retro_mmur_46,
Myotis lucifugus	ENSMLUG00000015299	1 retrocopy	retro_mluc_2,
Nomascus leucogenys	ENSNLEG00000016636	1 retrocopy	retro_nleu_622,
Pongo abelii	ENSPPYG00000019514	3 retrocopies	retro_pabe_2386 , retro_pabe_3548, retro_pabe_847,
Sorex araneus	ENSSARG00000012787	7 retrocopies	retro_sara_101, retro_sara_326, retro_sara_497, retro_sara_584, retro_sara_585, retro_sara_586, retro_sara_730,
Tupaia belangeri	ENSTBEG00000009011	2 retrocopies	retro_tbel_3123, retro_tbel_4170,