RetrogeneDB ID: retro_hsap_1532

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:20832669..20833956(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RNF145
• Ensembl ID: ENSG00000145860
• Aliases: None
• Description: ring finger protein 145 [Source:HGNC Symbol;Acc:20853]

Sequence

>retro_hsap_1532
GGTTATATCTTAAGTGTGGTGCTGCTAACATTGCCCAGGCAACATCTGGTTCAGCTTTATCTATATTTTTTGACTGCTCT
GCTTTTCTATACTGGACATCAAATTTCCAGGGACTACGTTCGGAGTGAACTGCAGTTTGCCTGTGAGGGACCAATGTATT
TAGAACCTCTCTCTATGAATCGGTTTACCACAGCCTTAATAGGTCAGTTGGTGGTGTGTACTTTATGCTCCTGTGTCATG
AAAACAAAGCAGATTTGGCTGTTTTCAGCTCACGTGCTTCCTCTGCTAGCACGACTCTGCCTGGTTCCTTTGGAGACAAT
TGTTATCATCAATAAATTTGCTATGATTTTTACTGGATTGGAAGTTCTCTATTTTCTTGGGTCTAATCTTTTGCTACCTT
ATAACCTTGCTAAATCTGCATACAGAGAATTGGTTCAGGTAGTGGAGGTATATGGCCTTCTCACCTTGGGAATGTCCTTG
TGGAATCAACTGGTAGTCCCTGTTCTTTTCATGGTTTTCTGGCTCATCTTATTTGCTCTTCAGATTTACTCCTATTTCAG
TACTCGAGATCAGCCGGCATCACGTGAGAGGCTTCTTTTCCTTTTTCTGACAAGTATTGCAGAATGCTGCAGCACTCCTT
ACTCTCTTTTGGGTTTGGTCTTCACGGTTTCTTTTGTTGCCTTGGGTGTTCTCACACTCTGCGAGTTTTACTTGCAGGGT
TATCGAGCTTTCAGGAATGATCCTGCCATGAATTGGGGCATGACAGGAGGAGTAACGCTGTTAATCCTGGCAGTGCAGAC
TGGGCTGATAGAACTGCAGGTTGTTCATCGGGCATTCCTGCTCAGTATTATCCTTTTCATTGTTGCAGCTTCTATCCTAC
AGTCTATGTTAGAAATTGCAGATCCTATTTTTTTGGCACTGGGAGCATCCAGAGACAAGAGCTTGTGGAAACACTTCCGT
GCTGTGCGACTTTGTTTATTTTTATTGGTATTCCCTGCTCATATGGCTTATATGATTTGCCAGTTTTTCCACCTGGATTT
TTGGCTTCTTATCATTATTTCCAGCAGCATTCTTACCTCTCTTCAGGTTCTGGGAACACTTTTTATTTATGTCTGATTTA
CGGTTGAGGAATTCAGAAAAGAGCCGGTGGAAAACATGGATGATGTCATCTACTATGTGAATGGCACTTACCACCTGCTG
GAGTTTCTTGCGGCCGTCTGTATGGTGGCCTATTGCGTCTCAGAGACCATCTTTGGAGAATGGACAGTGATGGGCTCAAT
GATCATC

Alignment

ORF - retro_hsap_1532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.41 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYILSVVLLTLPRQHLVQLYLYFLTALLLYAGHQISRDYVRSELEFAYEGPMYLEPLSMNRFTTALIGQL
          GYILSVVLLTLPRQHLVQLYLYFLTALL.Y.GHQISRDYVRSEL.FA.EGPMYLEPLSMNRFTTALIGQL
Retrocopy GYILSVVLLTLPRQHLVQLYLYFLTALLFYTGHQISRDYVRSELQFACEGPMYLEPLSMNRFTTALIGQL

Parental  VVCTLCSCVMKTKQIWLFSAHMLPLLARLCLVPLETIVIINKFAMIFTGLEVLYFLGSNLLVPYNLAKSA
          VVCTLCSCVMKTKQIWLFSAH.LPLLARLCLVPLETIVIINKFAMIFTGLEVLYFLGSNLL.PYNLAKSA
Retrocopy VVCTLCSCVMKTKQIWLFSAHVLPLLARLCLVPLETIVIINKFAMIFTGLEVLYFLGSNLLLPYNLAKSA

Parental  YRELVQVVEVYGLLALGMSLWNQLVVPVLFMVFWLVLFALQIYSYFSTRDQPASRERLLFLFLTSIAECC
          YRELVQVVEVYGLL.LGMSLWNQLVVPVLFMVFWL.LFALQIYSYFSTRDQPASRERLLFLFLTSIAECC
Retrocopy YRELVQVVEVYGLLTLGMSLWNQLVVPVLFMVFWLILFALQIYSYFSTRDQPASRERLLFLFLTSIAECC

Parental  STPYSLLGLVFTVSFVALGVLTLCKFYLQGYRAFMNDPAMNRGMTEGVTLLILAVQTGLIELQVVHRAFL
          STPYSLLGLVFTVSFVALGVLTLC.FYLQGYRAF.NDPAMN.GMT.GVTLLILAVQTGLIELQVVHRAFL
Retrocopy STPYSLLGLVFTVSFVALGVLTLCEFYLQGYRAFRNDPAMNWGMTGGVTLLILAVQTGLIELQVVHRAFL

Parental  LSIILFIVVASILQSMLEIADPIVLALGASRDKSLWKHFRAVSLCLFLLVFPAYMAYMICQFFHMDFWLL
          LSIILFIV.ASILQSMLEIADPI.LALGASRDKSLWKHFRAV.LCLFLLVFPA.MAYMICQFFH.DFWLL
Retrocopy LSIILFIVAASILQSMLEIADPIFLALGASRDKSLWKHFRAVRLCLFLLVFPAHMAYMICQFFHLDFWLL

Parental  IIISSSILTSLQVLGTLFIYVLFMVEEFRKEPVENMDDVIYYVNGTYRLLEFLVALCVVAYGVSETIFGE
          IIISSSILTSLQVLGTLFIYV.F.VEEFRKEPVENMDDVIYYVNGTY.LLEFL.A.C.VAY.VSETIFGE
Retrocopy IIISSSILTSLQVLGTLFIYV*FTVEEFRKEPVENMDDVIYYVNGTYHLLEFLAAVCMVAYCVSETIFGE

Parental  WTVMGSMII
          WTVMGSMII
Retrocopy WTVMGSMII

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	0.00 RPM	70.35 RPM
bodymap2_adrenal	0.00 RPM	103.90 RPM
bodymap2_brain	0.02 RPM	55.27 RPM
bodymap2_breast	0.00 RPM	77.45 RPM
bodymap2_colon	0.00 RPM	79.74 RPM
bodymap2_heart	0.00 RPM	26.68 RPM
bodymap2_kidney	0.00 RPM	60.90 RPM
bodymap2_liver	0.00 RPM	15.51 RPM
bodymap2_lung	0.04 RPM	170.22 RPM
bodymap2_lymph_node	0.00 RPM	120.31 RPM
bodymap2_ovary	0.00 RPM	119.13 RPM
bodymap2_prostate	0.00 RPM	92.28 RPM
bodymap2_skeletal_muscle	0.00 RPM	23.63 RPM
bodymap2_testis	0.00 RPM	66.36 RPM
bodymap2_thyroid	0.00 RPM	82.82 RPM
bodymap2_white_blood_cells	0.00 RPM	132.07 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1532 was not detected

EST

No EST(s) were mapped for retro_hsap_1532 retrocopy.

TSS

No TSS is located nearby retro_hsap_1532 retrocopy 5' end.

Lab

retro_hsap_1532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1532 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145860	2 retrocopies	retro_hsap_1532 , retro_hsap_1538,
Gorilla gorilla	ENSGGOG00000023385	1 retrocopy	retro_ggor_1171,
Nomascus leucogenys	ENSNLEG00000004241	1 retrocopy	retro_nleu_1745,