RetrogeneDB ID: retro_pabe_1560

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:52286873..52288535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSPPYG00000025848
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_pabe_1560
ATGGCGGCCTCAGCAAAAAAGAAGAATAAGAAGGGGAAGACTATCTCCCTAACAGACTTTCTGGCTGAGGATGGGGGTAC
TGGTGGAGGAAGCACCTATGTTTCCAAACCAGTCAGCTGGGCTGATGAAACGGATGACCTGGAAGGAGATGTTTCAACAA
CTTGGCACAGTAACGATGACGACGTGTATAGGGCGCCTCCAATTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTGCT
CGGGAACCCAATATCGACCGGAGCCGTCTTCCCAAATCGCCACCCTACACTGCTTTTCTAGGAAACCTACCCTATGATGT
TACAGAAGAGTCAATTAAGGAATTCTTTCGAGGATTAAATATCAGTGCAGTGCGTTTACCACGTGAACCCAGCAATCCAG
AGAGGTTGAAAGGTTTTGGTTATGCGGAATTTGAGGACCTGGATTCCCTGCTCAGTGCCCTGAGTCTCAATGAAGAGTCT
CTAGGTAACAGGAGAATTCGAGTGGACGTTGCTGATCAAGCACAGGATAAAGACAGGTATGATCGTTCTTTTGGCCGTGA
TAGAAATCGGGATTCTGACAAAACAGATACAGACTGGAGGGCTCGTCCTGCTACAGACAGCTTTGATGACTACCCACCTA
GAAGAGGTGATGATAGCTTTGGAGACAAGTATCGAGATCGTTATGATTCAGACCGGTATCGGGATGGGTATCGGGATGGA
TATCGGGATGGCCCACGCCGGGATATGGATCGATATGGTGGCCGGGATCGCTATGATGACCGAGGCAGCAGAAACTATGA
TAGAGGCTATGATTCCCGGATAGGCAGTGGCAGAAGAGCATTTGGCAGTGGGTATCGCAGGGATGATGACTACAGAGGAG
GCGGGGACGGCTATGAAGACCGATATGACAGACGGGATGATCGTTCGTGGAGCTCCAGAGATGATTACTCTCGGGATGAT
TATAGGCGTGATGATAGAGGTCCCCCCCAAAGACCCAAACTGAATCTAAAGCCTCGGAGTACTCCTAAGGAAGATGATTC
CTCTGCTAGTACCTCCCAGTCCACTCGAGCTGCTTCTATCTTTGGAGGGGAAAAGCCCGTTGACACAGCTGCTAGAGAAA
GAGAAGTAGAAGAACGGCTACAGAAGGAACAAGAGAAGTTGCAGCATCAGCTGGATGAGCCAAAACTAGAACGACGGCCT
CGGGAGAGACACCCAAGCTGGCGAAGTGAAGAAACTCAGGAACGGGAACGGTCAAGGACAGGAAGTGAGTCATCGCAGAC
TGGGACCTCCACCACATCTGGCAGAAATGCACGAAGGAGAGAGAGTGAGAAGTCTCTAGAAAATGAAACACTCAATAAGG
AGGAAGATTGCCACTCTCCAACTTCTAAACCTCCCAAACCTGATCAGCCCCTAAAGGTAATGCCATCCCCTCCACCAAAG
GAGAATGCTTGGGTGAAGTGAAGTTCTAACCCTCTTGCTCCATCTCAGAGCTCAGACACAGAGCAGCAATCCCCTACAAG
TGGTGGGGGAAAAGTAGCTCCAGCTCAACCCTCTGAGGAAGGACCAGCAAGGAAAGATTAAAATAAAGTAGATGGGATGA
ATGTCCCAAAAGGCCAAACTGGGAACTCTAGCCGTGGTCCAGGAGACGGAGGGAACAAAGAC

Alignment

ORF - retro_pabe_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 90.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDR
          MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDR
Retrocopy MAASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDR

Parental  SILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG
          SILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG
Retrocopy SILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG

Parental  YAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDD
          YAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDR.DRSFGRDRNRDSDKTDTDWRARPATDSFDD
Retrocopy YAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRYDRSFGRDRNRDSDKTDTDWRARPATDSFDD

Parental  YPPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRA
          YPPRRGDDSFGDKYRDRYDSD.............PRRDMDRYGGRDRYDDRGSR.YDRGYDSRIGSGRRA
Retrocopy YPPRRGDDSFGDKYRDRYDSDXXXXXXXXXXXXXPRRDMDRYGGRDRYDDRGSRNYDRGYDSRIGSGRRA

Parental  FGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSAS
          FGSGYRRDDDYRGGGD.YEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSAS
Retrocopy FGSGYRRDDDYRGGGDGYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSAS

Parental  TSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRT
          TSQSTRAASIFGG.KPVDTAAREREVEERLQKEQEKLQ.QLDEPKLERRPRERHPSWRSEETQERERSRT
Retrocopy TSQSTRAASIFGGEKPVDTAAREREVEERLQKEQEKLQHQLDEPKLERRPRERHPSWRSEETQERERSRT

Parental  GSESSQTGTSTTSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSN
          GSESSQTGTSTTSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMP.PPPKENAWVK.SSN
Retrocopy GSESSQTGTSTTSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPSPPPKENAWVK*SSN

Parental  PPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPARKDENKVDGMNVPKGQTGNSSRGPGDGGNKD
          P.A.SQSSDTEQQSPTSGGGKVAPAQPSEEGPARKD.NKVDGMNVPKGQTGNSSRGPGDGGNKD
Retrocopy PLAPSQSSDTEQQSPTSGGGKVAPAQPSEEGPARKD*NKVDGMNVPKGQTGNSSRGPGDGGNKD

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	2.99 RPM	52.30 RPM
SRP007412_cerebellum	1.70 RPM	30.52 RPM
SRP007412_heart	1.84 RPM	59.18 RPM
SRP007412_kidney	3.68 RPM	74.45 RPM
SRP007412_liver	1.99 RPM	56.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1560 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560 , retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,