RetrogeneDB ID: retro_hsap_640

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:131904309..131906715(+)
• Located in intron of: ENSG00000237489

Retrocopy information

• Ensembl ID: ENSG00000233122
• Aliases: CTAGE7P, CTAGE7, CTAGEP, bA500G10.2, rcCTAGE5
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CTAGE5
• Ensembl ID: ENSG00000150527
• Aliases: None
• Description: CTAGE family, member 5 [Source:HGNC Symbol;Acc:7057]

Sequence

>retro_hsap_640
ATGTTGGAGCCAGGGGCTACCCCTCAGCGGTACTTGGGGCTGGTCCTGGGGGAGCCACGCAGGGTTGTGGCAGCGCTGCC
TGAAAGTATGAGACTGGATTCGAATCCTCATGGTTTTCCATGGGAAATGGTGATATGTGCAGCTGTTGCTGCATTTTTTG
CTGTTCTCCTTTTTCTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAAGAGAGAAAAAGCTTGCTATA
ATGCTTTCTGGACTAATTGAAGAAAAATGTAAACTACTTGAAAAATTTAGCCTTGTTCAAAAAGAGTATGAAGACTATGA
AGTAGCGTCATCGTTAGAGGATGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTTGGAGGCAACCTGTGAAAAGT
TGAACAGGTCCAATTCTGAACTTGAGCATGAAATTCTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCG
CAACAAAATGAATTGATGGCGGATATTTCAAAAACGATACAGCCTCTAGCAGATGAGTCAGAATCCCTCAAATCACAAGT
AGCTGAAGCCAAAATGATCTTCAAGAGATTTAAAATGACTGAGAAACAACTGAAGATAGCAATAAAAGATGCTTTGAATG
AAAACTCTCACCTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAACGAACAAGTGAATGAACTTAAT
AAACAGAAAATAACATTTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCAAGACTCT
GACTGAACATTTGCTAAAGATGAAAGATTGGGCTGCTAGGCTTAGAGAAGACGTAACGGATGATGATAACTTAGAAGTGA
ACAGTGAATCAGAAGATGGTGCTTACTTAGATGATCCTCTAAAAGGAGCTCTGAAGAAACTGATTCATGCTACTAAGTTA
AATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTATATCCAGTTACCTGAAATTGATAAAACAAAGGAAGA
GCTTACAGAGCATATTAAAAATCTTCGGACTGAACAAGCATCTTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATC
AGAAGCTTCAACAGAAACTTAAAGTAATGACTGAATTATATCAAGAAAATGAAATGAAACTCTACAGGAAATTAACAGTA
GAGGAAAATAGCCGGTTAGAGAAAGAAGAGAAACTTTCTAAGGTAGACAAAAAGATCAGCCATGCCACTAAAGAGCTGGA
GACCTACAGACAGCGAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTATTCATTATTATCAACGGCAGATTATTTCCC
ATGAGAAAAAGGCACATCATAACTGGTTGGCAGCTTGGGCTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCT
CACAACAGACAAAAATTAGCTGAAACAGAGTATAAAATAAAACTTCTAAAAAAAGATCCTTATGTACTTGATGTTCCAAA
TACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCTCATCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTTTCTCT
CTCCCGCAACTCTGTTGGAGGGTCCACTCAGACTCTCACCTTTGCCTCCAGGGGGGGAAGGAAGAGGCTCAAGAGGCCCA
GGGAATCCTCTGGACCATCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGAAAGGTTAACCGATCCTCACAGGTCTCC
TTCTGACACTGGGTCCCTGTCACTTCCGAGGGAACAGGACCGTAGGATGATGTTTCCTCCACCAGCGCAATCATATCTTG
ATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAACTCTGGTGGACTGTCTGGACCAGCAGAACTCAGAAGT
TTTAATATGCCTCCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGACACCAAAGATGA
TCTTGGTAATTTAAATATCCCTGATTCATCTCTCCCTGCTGAAAATGCAGCAACTGGCCCTCGCTTTGTTCCTCCACCTC
TTGCCCTAATCAGAGGTCCACTGTTTCCAGTGGATACAAGGGGCCCGTTCATGAGAAGAGCACCTCCTTTCCCCCCACCT
CCTCCAGGAACCAGGTTTGGAGCTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCACATGCTCCGTTTGC
AATGAGAAATGTCTATCCACCGAGGGGTTTTCCTCCTTACCCTCCCCCAAGACCTGGATTTTTCCCCCGACCCCCACATT
CTGAAGGTAGAAGTGAGTTCCCTTCAGGGCTGATTCCGCCTTCAAATGAGCCTGCTACGGAACATCCAAAACCGCAGCAA
GATACC

Alignment

ORF - retro_hsap_640 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEPGVTPQPYLGLLLEELRRVVAALPEGMRPDSNLYGFPWELVICAAVVGFFAVLFFLWRSFRSVRSRL
          M.EPG.TPQ.YLGL.L.E.RRVVAALPE.MR.DSN..GFPWE.VICAAV..FFAVL.FLWRSFRSVRSRL
Retrocopy MLEPGATPQRYLGLVLGEPRRVVAALPESMRLDSNPHGFPWEMVICAAVAAFFAVLLFLWRSFRSVRSRL

Parental  YVGREKKLALMLSGLIEEKSKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSE
          YVGREKKLA.MLSGLIEEK.KLLEKFSLVQKEYE.YEV.SSL.DASFEK.A.EA.SLEATCEKLNRSNSE
Retrocopy YVGREKKLAIMLSGLIEEKCKLLEKFSLVQKEYEDYEVASSLEDASFEKAAAEARSLEATCEKLNRSNSE

Parental  LEDEILCLEKELKEEKSKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKD
          LE.EILCLEKELKEEKSKHS.Q.ELMADISK.IQ.L.DES.SLKSQVAEAKM.FK.F.M.E..LKIAIKD
Retrocopy LEHEILCLEKELKEEKSKHSQQNELMADISKTIQPLADESESLKSQVAEAKMIFKRFKMTEKQLKIAIKD

Parental  ALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSKVHAEQVLNDKESHIKTLTERLLKMKDWAAM
          ALNENS.LQESQKQLLQEAEVW.EQV.ELNKQK.TFEDSKVHAEQVLNDKE.HIKTLTE.LLKMKDWAA.
Retrocopy ALNENSHLQESQKQLLQEAEVWNEQVNELNKQKITFEDSKVHAEQVLNDKENHIKTLTEHLLKMKDWAAR

Parental  LGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEEL
          L.ED.TDDDNLE...NSESE.GAYLD.P.KGALKKLIHA.KLNASLKTLEGERNQIYIQL.E.DKTKEEL
Retrocopy LREDVTDDDNLEV--NSESEDGAYLDDPLKGALKKLIHATKLNASLKTLEGERNQIYIQLPEIDKTKEEL

Parental  TEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEK
          TEHIKNL.TEQASLQSENTHFE.ENQKLQQKLKVMTELYQENEMKL.RKLTVEEN.RLEKEEKLSKVD.K
Retrocopy TEHIKNLRTEQASLQSENTHFESENQKLQQKLKVMTELYQENEMKLYRKLTVEENSRLEKEEKLSKVDKK

Parental  ISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTE
          ISHAT.ELETYR.RAKDLEEELERTIH.YQ.QIISHEKKAH.NWLAA..AERNLNDLRKENAHNRQKL.E
Retrocopy ISHATKELETYRQRAKDLEEELERTIHYYQRQIISHEKKAHHNWLAAWAAERNLNDLRKENAHNRQKLAE

Parental  TELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSR
          TE.K..LL.KDPY.LDVPNTAFGREHSPYGPS.LG.PSSETRAFLSP.TLLEGPLRLSPL.PGG.GRGSR
Retrocopy TEYKIKLLKKDPYVLDVPNTAFGREHSPYGPSSLGRPSSETRAFLSPATLLEGPLRLSPLPPGGEGRGSR

Parental  GPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSN
          GPGNPLDHQIT.ERGESSC.RLTDPHR.PSDTGSLS.P..QDRRMMFPPP.QSY.DSALPPQRQDRF.SN
Retrocopy GPGNPLDHQITKERGESSCERLTDPHRSPSDTGSLSLPREQDRRMMFPPPAQSYLDSALPPQRQDRFYSN

Parental  SGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIR
          SG.LSGPAELRSFNMP.LDKMDGSMPSEMESSRNDTKDDLGNLN.PDSSLPAEN.ATGP.FVPPPLA.IR
Retrocopy SGGLSGPAELRSFNMPPLDKMDGSMPSEMESSRNDTKDDLGNLNIPDSSLPAENAATGPRFVPPPLALIR

Parental  GPLFPVDARGPFLRRGPPFPPPPPGAMFGASRDYFPPGDFPGPPPAPFAMRNVYPPRGFPPYLPPRPGFF
          GPLFPVD.RGPF.RR.PPFPPPPPG..FGASRDYFPPGDFPGPP.APFAMRNVYPPRGFPPY.PPRPGFF
Retrocopy GPLFPVDTRGPFMRRAPPFPPPPPGTRFGASRDYFPPGDFPGPPHAPFAMRNVYPPRGFPPYPPPRPGFF

Parental  PPPPHSEGRSEFPSGLIPPSNEPATEHPEPQQET
          P.PPHSEGRSEFPSGLIPPSNEPATEHP.PQQ.T
Retrocopy PRPPHSEGRSEFPSGLIPPSNEPATEHPKPQQDT

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	0.04 RPM	0.83 RPM
bodymap2_adrenal	0.27 RPM	1.68 RPM
bodymap2_brain	0.28 RPM	0.96 RPM
bodymap2_breast	0.14 RPM	1.09 RPM
bodymap2_colon	0.17 RPM	0.66 RPM
bodymap2_heart	0.04 RPM	0.63 RPM
bodymap2_kidney	0.74 RPM	2.83 RPM
bodymap2_liver	0.00 RPM	1.20 RPM
bodymap2_lung	0.23 RPM	0.95 RPM
bodymap2_lymph_node	1.50 RPM	0.91 RPM
bodymap2_ovary	0.52 RPM	1.41 RPM
bodymap2_prostate	0.74 RPM	1.11 RPM
bodymap2_skeletal_muscle	0.05 RPM	0.36 RPM
bodymap2_testis	2.39 RPM	1.64 RPM
bodymap2_thyroid	0.09 RPM	2.88 RPM
bodymap2_white_blood_cells	0.00 RPM	1.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_640 was not detected

EST

4 EST(s) were mapped to retro_hsap_640 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI461938	131904272	131904853	99.9	578	1	575
CV023017	131904309	131904985	99.6	666	2	658
DA027794	131904382	131904932	100	550	0	550
DB272697	131904535	131905092	100	557	0	557

TSS

No TSS is located nearby retro_hsap_640 retrocopy 5' end.

Lab

retro_hsap_640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_640 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_466
Pongo abelii	retro_pabe_29

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640 ,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,