RetrogeneDB ID: retro_hsap_4196

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:98908291..98910135(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224546
• 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_4196
GCGGCCTCAGCAAAAAAGAAGAAGAAGAAGGGGAAGACTATCTCCCTAACAGACTTTCTGGCTGAGGATGGGGGTACTGG
TGGAGGAAGGACCTATGTTTCCAAACCAGTCAGCTGAGCTGATGAAACGGATGACCTGGAAGGAGATGTTTCGACAACTT
GGCACAGTAACGATGACGATGTGTATAGGGCGTCTCCAATTGACCGTTCCATCCTTCCCACTGCTCCACGGGCTGCTCGG
GAACCCAATATCGACCGGAGCCATCTTCCCAAATCGCCACCCTACACTGCTTTTCTAGGAAACCTACCCTATGATGTTAC
AGAAGAGTCAATTAAGGAATTCTTTCGAGGATTAAATATCAGTGCAGTGCGTTTACCATGTGAACCCAGCAATCCAGTGA
GGTTGAAAGGTTTTGGTTATGCTGAATTTGAGGACCTGGATTCCCTGCTTAGTGCCCTGAGTCTCAAGGAAGAGTCTCTA
GGTAACAGGAGAATTCGAGTGGACGTTGCTGATCAAGCACAGGATAAAGACAGGGATGATTGTTCTTTTGGCCGTGATAG
AAATCGGGATTCTGACAAAACAGGTACAGACTGGAGGGCTCGTCCTGCTACAGACAGCTTTGATGACTACCCACCTAGAA
GAGGTGATGATAGCTTTGGAGACAAGTATCGAGATCGTTATGATTCAGACCGGTATCGGGATGGGTATCGGGATGGGTAT
CGGGATGGCCAACGCCGGGATATGGATCCATATGGTGGCCGGGATCGCTATGATGACCGAGGCAGCAGAGACTATGATAG
AGGCTATGATTCCCGGATAGGCAGTGGCAGAAGAGCATTTGGCAGTGGGTATCGCAGGGATGATGTCTCAGAGGAGGCGG
GGACCACTATGAAGACCGATATGACAGACGGGATGATCGGTCTTGGAGCTCCAGAGATGATTACTCTCTGGATGATTATA
GGCGTGATGGTAGAGGTCCCCCCCAAAGACCCAAACTGAATCTAAACCCTCGGAGTACTCCTAAGGAAGATGATTCCTCT
GCTAGTACCTCCCAGTCCACTCGAGCTGCTTCTATCTTTGGAGGGGCAAAGCCCGTTGACACAGCTGCTAGAGAAAGAGA
AGTAGAAGAACGGCTACAGAAGGAACAAGAGAAGTTGCAGCATCAGCTGGATGAGCCAAAACTAGAACGACGGCCTCCGG
AGAGACACCCAAGCTGGCGAAGTGAAGAAACTCAGGAACGGGAACGGTCGAGGACAGGAAGTGAGTCATCACAGACTGGG
ACCTCCACCACATCTGGCAGAAGTAAGTCAGCCCAGGATGCACGAAGGAGAGAGAATGAGAAGTCTCTAGAAAATGAAAC
ACTCAATAAGGAGGAAGATTGCCACTCTCCAACTTCTAAACCTCCCAAACCTGATCAGCCCCTAAAGGTAATGCCAGCCC
CTCCACCAAAGGAGAATGCTTGGGTGAAGCGAAGTTCTAACCCTCCTGCTCGATCTCAGAGCTCAGACACAGAGCAGCAA
TCCCCTACAAGTGGTGAGGGAAAAGTAGCTCCAGCTCAACCATCTGAGGAAGGACCAGCAAGGAAAGATGAAAACAAAGT
AGATGGGATGAATGTCCCAAAAGGCCAAACTGGGAACTCTAGCCGTGGTCCAGGAGATGGAGGGAACAAAGACCACTGGA
AGGAGTCAGATAGGAAAGATGGCAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTGAGGAAAATCCA
GCTTCCAAGTTCAGTTCTGCAAGCAAGTATGCTGCTCTCTCTGTTGATGGTGAAGATGAAAATGAGGGAGAAGATTATGC
CGAA

Alignment

ORF - retro_hsap_4196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.34 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AASAKKKNKKGKTISLTDFLAEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRS
          AASAKKK.KKGKTISLTDFLAEDGGTGGG.TYVSKPVS.ADETDDLEGDVSTTWHSNDDDVYRA.PIDRS
Retrocopy AASAKKKKKKGKTISLTDFLAEDGGTGGGRTYVSKPVS*ADETDDLEGDVSTTWHSNDDDVYRASPIDRS

Parental  ILPTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY
          ILPTAPRAAREPNIDRS.LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLP.EPSNP.RLKGFGY
Retrocopy ILPTAPRAAREPNIDRSHLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPCEPSNPVRLKGFGY

Parental  AEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDY
          AEFEDLDSLLSALSL.EESLGNRRIRVDVADQAQDKDRDD.SFGRDRNRDSDKT.TDWRARPATDSFDDY
Retrocopy AEFEDLDSLLSALSLKEESLGNRRIRVDVADQAQDKDRDDCSFGRDRNRDSDKTGTDWRARPATDSFDDY

Parental  PPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAF
          PPRRGDDSFGDKYRDRYDSD..............RRDMD.YGGRDRYDDRGSRDYDRGYDSRIGSGRRAF
Retrocopy PPRRGDDSFGDKYRDRYDSDXXXXXXXXXXXXXQRRDMDPYGGRDRYDDRGSRDYDRGYDSRIGSGRRAF

Parental  GSGYRRDDD-YRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSAS
          GSGYRRDD...RGGGD.YEDRYDRRDDRSWSSRDDYS.DDYRRD.RGPPQRPKLNL.PRSTPKEDDSSAS
Retrocopy GSGYRRDDV<LRGGGDHYEDRYDRRDDRSWSSRDDYSLDDYRRDGRGPPQRPKLNLNPRSTPKEDDSSAS

Parental  TSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRT
          TSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQ.QLDEPKLERRP.ERHPSWRSEETQERERSRT
Retrocopy TSQSTRAASIFGGAKPVDTAAREREVEERLQKEQEKLQHQLDEPKLERRPPERHPSWRSEETQERERSRT

Parental  GSESSQTGTSTTSSRSKSDQDARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWV
          GSESSQTGTSTTS.RSKS.QDARRRE.EKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWV
Retrocopy GSESSQTGTSTTSGRSKSAQDARRRENEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWV

Parental  KRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPGRKDENKVDGMNAPKGQTGNSSRGPGDGGNRDH
          KRSSNPPARSQSSDTEQQSPTSG.GKVAPAQPSEEGP.RKDENKVDGMN.PKGQTGNSSRGPGDGGN.DH
Retrocopy KRSSNPPARSQSSDTEQQSPTSGEGKVAPAQPSEEGPARKDENKVDGMNVPKGQTGNSSRGPGDGGNKDH

Parental  WKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
          WKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
Retrocopy WKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE

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	0.20 RPM	703.14 RPM
bodymap2_adrenal	0.27 RPM	434.24 RPM
bodymap2_brain	0.05 RPM	232.88 RPM
bodymap2_breast	0.19 RPM	442.03 RPM
bodymap2_colon	0.54 RPM	722.93 RPM
bodymap2_heart	0.20 RPM	297.04 RPM
bodymap2_kidney	0.10 RPM	206.91 RPM
bodymap2_liver	0.17 RPM	106.15 RPM
bodymap2_lung	0.00 RPM	407.72 RPM
bodymap2_lymph_node	0.37 RPM	454.43 RPM
bodymap2_ovary	0.54 RPM	1147.94 RPM
bodymap2_prostate	0.24 RPM	826.01 RPM
bodymap2_skeletal_muscle	1.24 RPM	1007.06 RPM
bodymap2_testis	0.23 RPM	372.14 RPM
bodymap2_thyroid	0.21 RPM	489.01 RPM
bodymap2_white_blood_cells	1.14 RPM	716.99 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4196 was not detected

EST

No EST(s) were mapped for retro_hsap_4196 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_195254	434 libraries	739 libraries	643 libraries	10 libraries	3 libraries

The graphical summary, for retro_hsap_4196 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4196 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,