RetrogeneDB ID: retro_hsap_96

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:103907550..103908741(+)
• Located in intron of: ENSG00000170962

Retrocopy information

• Ensembl ID: ENSG00000170967
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDI2
• Ensembl ID: ENSG00000197312
• Aliases: None
• Description: DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]

Sequence

>retro_hsap_96
ATGCTGATCACCGTGTACTGCGTGCGGAGGGACCTCTCCGAGGTCACCTTCTCTCTCCAGGTCAGCCCCGACTTTGAGCT
CCGAAACTTCAAGGTCCTCTGCGAAGCGGAGTCCAGAGTCCCCGTCGAAGAGATCCAGATCATCCACATGGAGCGACTCC
TCATCGAGGACCACTGTTCCCTGGGCTCCTACGGCCTCAAAGATGGCGATATCGTGGTTTTACTGCAGAAGGACAATGTG
GGACCTCGGGCTCCAGGGCGTGCCCCGAACCAGCCTCGTGTAGACTTCAGTGGCATTGCGGTGCCTGGGACGTCCAGCTC
CCGTCCACAGCACCCTGGACAGCAGCAGCAGCGCACACCCGCTGCCCAGCGGTCACAGGGCTTGGCGTCAGGAGAGAAGG
TGGCCGGCCTGCAAGGTCTGGGCAGCCCCGCCCTGATCCGCAGCATGCTGCTCTCCAACCCCCACGATCTGTCCCTGCTC
AAGGAACGCAACCCTCCCTTGGCGGAAGCCCTGCTCAGCGGAAGCCTTGAGACCTTTTCTCAGGTGCTGATGGAGCAGCA
AAGGGAAAAGGCCTTGAGAGAGCAAGAGAGGCTTCGTCTCTACACAGCCGACCCACTGGATCGGGAAGCTCAGGCCAAAA
TAGAAGAGGAAATCCGGCAGCAAAACATTGAAGAAAACATGAATATAGCGATAGAAGAGGCCCCCGAGAGTTTTGGACAA
GTGACGATGCTCTACATTAACTGCAAAGTGAATGGGCATCCTTTGAAGGCTTTTGTTGACTCGGGCGCCCAGATGACCAT
TATGAGCCAGGCTTGTGCCGAGCGATGTAACATCATGAGGCTGGTGGACCGACGGTGGGCTGGGGTTGCTAAAGGAGTGG
GCACACAGAGAATTATTGGCCGTGTTCATCTAGCTCAGATTCAAATTGAAGGTGATTTCTTACAGTGCTCTTTCTCCATA
CTTGAGGATCAACCCATGGATATGCTTCTAGGCCTAGATATGCTCCGGAGACATCAATGTTCCATCGATTTGAAGAAAAA
TGTGCTGGTCATCGGCACCACTGGCACGCAGACTTATTTTCTTCCTGAGGGAGAGTTGCCCTTATGCTCTAGGATGGTAA
GTGGGCAAGATGAGTCTTCGGACAAGGAAATTACACATTCAGTCATGGATTCAGGACGAAAAGAGCATTAA

Alignment

ORF - retro_hsap_96 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.7 %
• Parental protein coverage: 73.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQKENADPRPPVQFPNLPRIDFSSIAVPGTSSPRQRQPPGTQQSHSSPGEITSSPQGLDNPALLRDMLLA
          R....A...P.V.F........SS..........QR.P..........GE.....QGL..PAL.R.MLL.
Retrocopy RAPGRAPNQPRVDFSGIAVPGTSSSRPQHPGQQQQRTPAAQRSQGLASGEKVAGLQGLGSPALIRSMLLS

Parental  NPHELSLLKERNPPLAEALLSGDLEKFSRVLVEQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQN
          NPH.LSLLKERNPPLAEALLSG.LE.FS.VL.EQQ...A.REQER.RL..ADP.D.EAQAKIEE.IRQQN
Retrocopy NPHDLSLLKERNPPLAEALLSGSLETFSQVLMEQQREKALREQERLRLYTADPLDREAQAKIEEEIRQQN

Parental  IEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKG
          IEENM.IA.EEAPESFGQV.MLYINCKVNGHP.KAFVDSGAQMTIMSQACAERCNIMRLVDRRWAG.AKG
Retrocopy IEENMNIAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKG

Parental  VGTQKIIGRVHLAQVQIEGDFLPCSFSILEEQPMDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTTFLP
          VGTQ.IIGRVHLAQ.QIEGDFL.CSFSILE.QPMDMLLGLDML.RHQCSIDLKKNVLVIGTTG.QT.FLP
Retrocopy VGTQRIIGRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSIDLKKNVLVIGTTGTQTYFLP

Parental  EGELPECARLAYG
          EGELP.C.R...G
Retrocopy EGELPLCSRMVSG

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	0.14 RPM	91.52 RPM
bodymap2_adrenal	0.00 RPM	46.55 RPM
bodymap2_brain	0.02 RPM	36.12 RPM
bodymap2_breast	0.00 RPM	80.60 RPM
bodymap2_colon	0.00 RPM	34.13 RPM
bodymap2_heart	0.09 RPM	45.99 RPM
bodymap2_kidney	0.00 RPM	58.69 RPM
bodymap2_liver	0.00 RPM	62.50 RPM
bodymap2_lung	0.00 RPM	51.65 RPM
bodymap2_lymph_node	0.00 RPM	52.30 RPM
bodymap2_ovary	0.00 RPM	54.13 RPM
bodymap2_prostate	0.00 RPM	51.72 RPM
bodymap2_skeletal_muscle	0.00 RPM	279.40 RPM
bodymap2_testis	20.95 RPM	35.58 RPM
bodymap2_thyroid	0.00 RPM	43.56 RPM
bodymap2_white_blood_cells	0.08 RPM	68.08 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_96 was not detected

EST

4 EST(s) were mapped to retro_hsap_96 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA383522	103907942	103908125	100	182	0	181
CV024159	103907550	103908169	99.6	614	3	611
CV024181	103907550	103908112	100	561	0	561
HY014386	103907501	103908004	99.9	502	1	501

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_9125	1826 libraries	0 libraries	0 libraries	1 library	2 libraries
TSS #2	TSS_9126	1825 libraries	1 library	0 libraries	0 libraries	3 libraries

The graphical summary, for retro_hsap_96 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_96 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_96 has 11 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_570
Gorilla gorilla	retro_ggor_143
Pongo abelii	retro_pabe_158
Macaca mulatta	retro_mmul_231
Callithrix jacchus	retro_cjac_196
Mus musculus	retro_mmus_67
Oryctolagus cuniculus	retro_ocun_249
Bos taurus	retro_btau_15
Sus scrofa	retro_sscr_6
Canis familiaris	retro_cfam_193
Equus caballus	retro_ecab_110

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15, retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96 ,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,