RetrogeneDB ID: retro_pabe_10

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:10800216..10801635(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000004275
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EIF2S3
• Ensembl ID: ENSPPYG00000020194
• Aliases: None
• Description: eukaryotic translation initiation factor 2 subunit 3 [Source:RefSeq peptide;Acc:NP_001125875]

Sequence

>retro_pabe_10
ATGGCGGGCGGAGAAGCTGGAGTGATTCTGCGGCAGCCGCATCTTTCGCGTCAGGATCTCACCACCTTGGATGTTACCAA
GTTGACGCCACTTTCACACGAAGTTATCAGCAGACAAGCCACAATTAATATAGGTACAATTGGTCATGTAGCTCATGGGA
AATCCACAGTAGTCAAAGCTATTTCTGGAGTTCACACCGTCAGGTTCAAAAATGAACTAGAAAGAAATATTACAATCAAG
CTTGGATATGCTAATGCTAAGATTTATAAACTTGATGACCCAAGTTGCCCTCGGCCAGAATGTTATCGATCTTGTGGGAG
CGGTACGGCTGATGAGTTTCCTACAGACATTCCAGGGACCAAAGGGAACTTCAAATTAGTCAGACATGTTTCCTTTGTTG
ACTGTCCTGGCCACGATATTTTGATGGCTACTATGCTGAACGGTGCAGCAGTGATGGATGCAGCTCTTCTGTTGATAGCT
GGTAATGAATCTTGCCCTCAGCCTCAGACATCTGAACACCTGGCTGCTATAGAGATCATGAAACTGAAGCATATTTTGAT
TCTACAAAATAAAATTGATTTGGTAAAAGAAAGTCAGGCTAAAGAACAATACGAGCAGATCCTTGCATTTGTCCAAGGTA
CAGTAGCAGAGGGAGCTCCCATTATTCCAATTTCGGCTCAGCTGAAATACAATATTGAAGTTGTTTGTGAGTACATAGTA
AAGAAAATTCCAGTACCCCCAAGAGACTTTACTTCAGAGCCCCGGCTTATTGTTATTAGATCTTTTGATGTCAACAAACC
TGGCTGTGAAGTTGATGACCTTAAGGGAGGTGTAGCTGGTGGTAGTATCCTAAAAGGAGTATTAAAGGTGGGCCAGGAGA
CAGAAGTAAGACCTGGTATTGTTTCCAAAGATAGTGAAGGAAAACTCATGTGTAAACCAATCTTTTCCAAAATTGTTTCA
CTTTTTGCGGAGCATAATGATCTGCAATATGCTGCTCCAGGCGGTCTTATTGGAGTTGGAACAAAAATTGACCCCACTTT
GTGCCGGGCTGACAGAATGGTGGGGCAAGTACTTGGTGCAATCGGAGCTTTACCTGAGATATTCACAGAATTGGAAATTT
CCTATTTCCTGCTTAGACGGCTTCTAGGTGTACGCACTGAAGGAGACAAGAAAGCAGCAAAGGTTCAAAAGCTGTCTAAG
AATGAAGTGCTCATGGTGAACATAGGATCCCTGTCGACAGGAGGGAGAGTTAGTGCTGTCAAGGCTGATTTGGGTAAAAT
TGTTTTGACCAATCCAGTGTGCACAGAGGTAGGAGAAAAAATTGCCCTTAGCCGAAGAGTTGAAAAACACTGGCGTTTAA
TTGGTTGGGGTCAGATAAGAAGAGGAGTGACAATCAACCCAACAGTAGATGATGACTGA

Alignment

ORF - retro_pabe_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK
          MAGGEAGV.L.QPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK
Retrocopy MAGGEAGVILRQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK

Parental  NELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDI
          NELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGS.T.DEFPTDIPGTKGNFKLVRHVSFVDCPGHDI
Retrocopy NELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSGTADEFPTDIPGTKGNFKLVRHVSFVDCPGHDI

Parental  LMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAF
          LMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAF
Retrocopy LMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAF

Parental  VQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAG
          VQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAG
Retrocopy VQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAG

Parental  GSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRA
          GSILKGVLKVGQE.EVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRA
Retrocopy GSILKGVLKVGQETEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRA

Parental  DRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAV
          DRMVGQVLGA.GALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAV
Retrocopy DRMVGQVLGAIGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAV

Parental  KADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD
          KADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTI.PTVDDD
Retrocopy KADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTINPTVDDD

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	0.06 RPM	58.50 RPM
SRP007412_cerebellum	0.24 RPM	45.24 RPM
SRP007412_heart	0.12 RPM	37.87 RPM
SRP007412_kidney	0.17 RPM	89.50 RPM
SRP007412_liver	0.15 RPM	53.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_10 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_10 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_10 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10 ,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,