RetrogeneDB ID: retro_hsap_309

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:220426911..220427880(+)
• Located in intron of: ENSG00000118873

Retrocopy information

• Ensembl ID: ENSG00000218283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MORF4L1
• Ensembl ID: ENSG00000185787
• Aliases: MORF4L1, Eaf3, HsT17725, MEAF3, MORFRG15, MRG15, S863-6
• Description: mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]

Sequence

>retro_hsap_309
ATGGCGCGGAAGCAGGACCCGAAGCCTAAATTCCAGGAGGGTGAGCGAGTGCTGTGCTTTCATGGGCCTCTTCTTTATGA
AGCAAAGTGTGTAAAGGTTGCCATAAAGGACAAACAAGTGAAATACTTCATACATTACAGTGGTTGGAATAAAAATTGGG
ATGAGTGGGTTCCGGAGAGCAGAGTACTCAAATACGTGGACACCAATTTGCAGAAACAGCGAGAACTTCAAAAAGCCAAT
CAGGAGCAGTATGCAGAGGGGAAGATGAGAGGGGCTGCCCCAGGAAAGAAGACATCTGGTCTGCAACAGAAAAATGTTGA
AGTGAAAACGAAAAAGAACAAACAGAAAACACCTGGAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTT
GGAAGAAAAGGGCCCGGGTAGATCCTACTGTTGAAAATGAGGAAACATTCATGAACAGAGTTGAAGTTAAAGTAAAGATT
CCTGAATAGCTAAAACCGTGGCTTGTTGATGACTGGGACTTAATTACCAGGCAAAAACAGCTCTTTTATCTTCCTGCCAA
GAAGAATGTGGATTCCATTCTTGAGGATTATGCAAATTACAAGAAATCTCGTGGAAACACAGATAATAAGGAGTATGCGG
TTAATGAAGTTGTGGCAGGGATAAAAGAATACTTCAACGTAATGTTGGGTACCCAGCTACTCTATAAATTTGAGAGACCA
CAGTATGCCGAAATTCTTGCAGATCATCCCGATGCACCCATGTCCCAGGTGTATGGAGCGCCACATCTCCTGAGATTATT
TGTACGAATTGGAGCAATGTTGGCCTATACACCTCTGGATGAGAAGAGCCTTGCTTTATTACTCAATTATCTTCACGATT
TCCTAAAGTACCTGGCAAAGAATTCTGCAACTTTGTTTAGTGCCAGCGATTATGAAGTGGCTCCTCCTGAGTACCATCGG
AAAGCTGTG

Alignment

ORF - retro_hsap_309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
          MA.KQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
Retrocopy MARKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL

Parental  QKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRARV
          QKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPP.KKRARV
Retrocopy QKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPWKKRARV

Parental  DPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK
          DPTVENEETFMNRVEVKVKIPE.LKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK
Retrocopy DPTVENEETFMNRVEVKVKIPE*LKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNK

Parental  EYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLD
          EYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLD
Retrocopy EYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLD

Parental  EKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
          EKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
Retrocopy EKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV

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	11.73 RPM	403.50 RPM
bodymap2_adrenal	9.05 RPM	314.53 RPM
bodymap2_brain	15.07 RPM	505.20 RPM
bodymap2_breast	9.30 RPM	354.28 RPM
bodymap2_colon	12.59 RPM	440.61 RPM
bodymap2_heart	14.09 RPM	229.42 RPM
bodymap2_kidney	5.77 RPM	281.27 RPM
bodymap2_liver	3.97 RPM	94.40 RPM
bodymap2_lung	16.37 RPM	367.95 RPM
bodymap2_lymph_node	7.64 RPM	255.39 RPM
bodymap2_ovary	15.69 RPM	497.94 RPM
bodymap2_prostate	13.39 RPM	338.07 RPM
bodymap2_skeletal_muscle	12.22 RPM	209.69 RPM
bodymap2_testis	20.19 RPM	608.48 RPM
bodymap2_thyroid	15.10 RPM	443.38 RPM
bodymap2_white_blood_cells	9.43 RPM	243.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_309 was not detected

EST

No EST(s) were mapped for retro_hsap_309 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_89956	909 libraries	650 libraries	256 libraries	10 libraries	4 libraries
TSS #2	TSS_89957	295 libraries	448 libraries	931 libraries	126 libraries	29 libraries

The graphical summary, for retro_hsap_309 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_309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_309 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012344	1 retrocopy	retro_amel_124,
Bos taurus	ENSBTAG00000010988	1 retrocopy	retro_btau_137,
Canis familiaris	ENSCAFG00000014113	1 retrocopy	retro_cfam_20,
Callithrix jacchus	ENSCJAG00000002214	5 retrocopies	retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Homo sapiens	ENSG00000185787	3 retrocopies	retro_hsap_309 , retro_hsap_3125, retro_hsap_850,
Gorilla gorilla	ENSGGOG00000016826	3 retrocopies	retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Macaca mulatta	ENSMMUG00000022926	1 retrocopy	retro_mmul_1064,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Mustela putorius furo	ENSMPUG00000015429	1 retrocopy	retro_mputfur_180,
Mus musculus	ENSMUSG00000062270	9 retrocopies	retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys	ENSNLEG00000008678	3 retrocopies	retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus	ENSOCUG00000015117	2 retrocopies	retro_ocun_108, retro_ocun_21,
Otolemur garnettii	ENSOGAG00000006047	4 retrocopies	retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii	ENSPPYG00000006703	4 retrocopies	retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes	ENSPTRG00000007351	3 retrocopies	retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus	ENSRNOG00000014410	6 retrocopies	retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Sus scrofa	ENSSSCG00000001769	1 retrocopy	retro_sscr_93,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608,