RetrogeneDB ID: retro_pabe_1600

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:62477473..62478364(-)
• Located in intron of: ENSPPYG00000009155

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC2
• Ensembl ID: ENSPPYG00000018820
• Aliases: EMC2, TTC35
• Description: ER membrane protein complex subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R882]

Sequence

>retro_pabe_1600
ATGGCGAAGGTCTCAGAGCTTTACGATGTCACTTGGGAAGAAATGAGAGATAAAATGAGAAAATGGAGAGAAGAAAACTC
AAGAAATAGTGAGCAAATTGTGGAAGTTGGAGAAGAATTAATTAATGAATATGGTTCTAAGCTGGGAGATGATATTTGGA
TCATATATGAACAGGTGATGATTGCAGCACTAGACTATGGTCGGGATGACTTGGCATTGTTTTGTCTTCAAGAGCTAAGA
AGACAGTTCCCTGGCAGTCACAGAGTCAAGCGATTAACAGGCATGAGATTTGAAGCCATGGAAAGATATGATGATGCTAT
ACAGCTATATGATAGGATTTTACAAGAAGATCCAACTAACACTGCTGCAAGAAAGCGTAAGATTGCCATTCGAAAAGCCC
AGGGGAAAAATGTGGAGGCCATTCGGGAGCTGAATGAGTATCTGGAACAATTTGTTGGAGACCAAGAAGCCTGGCATGAA
CTTGCAGAACTTTACATCAATGAACATGACTATGCAAAAGCAGCCTTTTGTTTAGAGGAACTAATGATGACTAATCCACA
CAACCACTTATACTGTCAGCAGTATGCTGAAGTTAAGTATACCCAAGGTGGACTTGAAAACCTCGAACTTTCAAGAAAGT
ATTTTGCACAGGCATTGAAACTGAACAACAGAAATATGAGAGCTTTGTTTGGGCTTTATATGTCGGCAAGTCATATTGCT
TCTAATCCAAAAGCAAGTGCAAAAACGAAAAAGGACAACATGAAATATGCTAGTTGGGCAGCTAGTCAAATAAACAGAGC
TTATCAGTTTGCAGGTCGAAGTAAGAAGGAATCCAAATATTCTCTTAAGGCTGTCGAAGACATGTTGGAAACATTGCAGA
TCATCCAGTCT

Alignment

ORF - retro_pabe_1600 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYGSKLGDDIWIIYEQVMIAALDYGRDD
          MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYGSKLGDDIWIIYEQVMIAALDYGRDD
Retrocopy MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYGSKLGDDIWIIYEQVMIAALDYGRDD

Parental  LALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQGKNVEA
          LALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQGKNVEA
Retrocopy LALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQGKNVEA

Parental  IRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLEL
          IRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLEL
Retrocopy IRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLEL

Parental  SRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETKY
          SRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKE.KY
Retrocopy SRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKESKY

Parental  SLKAVEDMLETLQITQS
          SLKAVEDMLETLQI.QS
Retrocopy SLKAVEDMLETLQIIQS

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	14.21 RPM
SRP007412_cerebellum	0.12 RPM	21.77 RPM
SRP007412_heart	1.11 RPM	12.10 RPM
SRP007412_kidney	0.46 RPM	14.02 RPM
SRP007412_liver	0.12 RPM	9.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1600 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1600 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012826	1 retrocopy	retro_amel_600,
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726,
Choloepus hoffmanni	ENSCHOG00000011271	3 retrocopies	retro_chof_1512, retro_chof_1990, retro_chof_851,
Callithrix jacchus	ENSCJAG00000006437	2 retrocopies	retro_cjac_3295, retro_cjac_3867,
Myotis lucifugus	ENSMLUG00000013258	2 retrocopies	retro_mluc_2369, retro_mluc_2452,
Mustela putorius furo	ENSMPUG00000005915	1 retrocopy	retro_mputfur_1647,
Mus musculus	ENSMUSG00000022337	1 retrocopy	retro_mmus_1262,
Oryctolagus cuniculus	ENSOCUG00000002461	1 retrocopy	retro_ocun_1251,
Pongo abelii	ENSPPYG00000018820	1 retrocopy	retro_pabe_1600 ,