RetrogeneDB ID: retro_hsap_4891

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:110862947..110864087(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000225031
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSG00000063046
• Aliases: EIF4B, EIF-4B, PRO1843
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_hsap_4891
AGAAGAGGTGATGATAGCTTTGGAGACAAGTATCGGGATCGTTATGATTCAGACCGGTATCGGGATGGGTATCGGGATGG
CCCACGCCGGGATATGGATGGATATGGTGGCCGGGATCGCTATGATGACCAAGGCAGCAGAGACTATGATAGAGGCTATG
ATTCCCGGATAGGCAGTGGCAGAAGAGCATTTGGCAGCGGGTATCGCAGGGATGATGACTACAGAGGAGGCGGGGACCGC
TATGAAGACTGATATGACAGACGGGATGATCGGTCGTGGAGCTCCAGAGATGATTACTCTCGGGATGATTATAGGTGTGA
TGATAGACGTCCCCCCCAAAGACCCAAACTGAATCTAAAGCCTTGGAGTACTCTTAAGCAAGATGATTCCTCTGCTAGTA
CCTCCCAGTCCACTCGAGCTGCTTCTATCTTTGGAGGGGCAAAGCCTGTTGACACAGCTGCTAGAGAAAGAGAAGTAGAA
GAACGGCTACAGAAGGAACAAGAGAAGTTGCAGCGTCAGCTGAGTGAGCCAAAACTAGAACGACGGCCTCGGGAGAGACA
CCCAAGCTGGCGAAGTGAAGAAACTCAGGAACGGGAACGGTCAAGGACAGGAAGTGAGTCATCGCAGACTGGGACCTCCA
CCACATCTGGCAGAAATGCACGAAGGAGAGAGAGTAAGAAGTCTCTAGAAAATGAAACACTCAATAAGGAGGAAGATTGC
CACTCTCCAACTTCTAAACCTCCCAAACCTGATCAGCCCCTAAAGGTAATGCCAGCCCCTCCACCAAAGGAGAATGCTTG
GGTGAAGCGAAGTTCTAACCCTCCTGCTCGATCTCAGAGCTCAGACGCAGAGCAGCAATCCCCTACAAGTGGTGGGGGAA
AAGTAGCTCCAGCTCAACCATCTGAGGAAGGACCAGCAAGGCAAGATGAAAATAAAGTAGATGGGATGAATGTCCCAAAA
GGCCAAACTGGGAACTCTAGCCGTGGTCCAGGAGACGGAGGGAACAAAGACCACTGGAAGGAGTCAGATAGGAAAGATGG
CAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTGAGGAAAATCCAGCTTCCAAGTTCAGTTCTGCAA
GCAACTATGCTGCTCTCTCT

Alignment

ORF - retro_hsap_4891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 67.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGS
          RRGDDSFG....D.Y......D.........PRRDMD.YGGRDRYDD.GSRDYDRGYDSRIGSGRRAFGS
Retrocopy RRGDDSFG----DKYRDRYDSDXXXXXXXXXPRRDMDGYGGRDRYDDQGSRDYDRGYDSRIGSGRRAFGS

Parental  GYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQ
          GYRRDDDYRGGGDRYED.YDRRDDRSWSSRDDYSRDDYR.DDR.PPQRPKLNLKP.ST.K.DDSSASTSQ
Retrocopy GYRRDDDYRGGGDRYED*YDRRDDRSWSSRDDYSRDDYRCDDRRPPQRPKLNLKPWSTLKQDDSSASTSQ

Parental  STRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRTGSE
          STRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQL.EPKLERRPRERHPSWRSEETQERERSRTGSE
Retrocopy STRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLSEPKLERRPRERHPSWRSEETQERERSRTGSE

Parental  SSQTGTSTTSSRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPA
          SSQTGTSTTS.RNARRRES.KSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPA
Retrocopy SSQTGTSTTSGRNARRRESKKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPA

Parental  RSQSSDTEQQSPTSGGGKVAPAQPSEEGPGRKDENKVDGMNAPKGQTGNSSRGPGDGGNRDHWKESDRKD
          RSQSSD.EQQSPTSGGGKVAPAQPSEEGP.R.DENKVDGMN.PKGQTGNSSRGPGDGGN.DHWKESDRKD
Retrocopy RSQSSDAEQQSPTSGGGKVAPAQPSEEGPARQDENKVDGMNVPKGQTGNSSRGPGDGGNKDHWKESDRKD

Parental  GKKDQDSRSAPEPKKPEENPASKFSSASKYAALS
          GKKDQDSRSAPEPKKPEENPASKFSSAS.YAALS
Retrocopy GKKDQDSRSAPEPKKPEENPASKFSSASNYAALS

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
bodymap2_adipose	8.09 RPM	703.14 RPM
bodymap2_adrenal	3.68 RPM	434.24 RPM
bodymap2_brain	1.64 RPM	232.88 RPM
bodymap2_breast	3.81 RPM	442.03 RPM
bodymap2_colon	6.77 RPM	722.93 RPM
bodymap2_heart	1.42 RPM	297.04 RPM
bodymap2_kidney	1.28 RPM	206.91 RPM
bodymap2_liver	0.17 RPM	106.15 RPM
bodymap2_lung	1.18 RPM	407.72 RPM
bodymap2_lymph_node	1.17 RPM	454.43 RPM
bodymap2_ovary	13.26 RPM	1147.94 RPM
bodymap2_prostate	1.51 RPM	826.01 RPM
bodymap2_skeletal_muscle	3.36 RPM	1007.06 RPM
bodymap2_testis	3.71 RPM	372.14 RPM
bodymap2_thyroid	3.94 RPM	489.01 RPM
bodymap2_white_blood_cells	2.03 RPM	716.99 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4891 was not detected

EST

No EST(s) were mapped for retro_hsap_4891 retrocopy.

TSS

No TSS is located nearby retro_hsap_4891 retrocopy 5' end.

Lab

retro_hsap_4891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 41 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	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,