RetrogeneDB ID: retro_hsap_4281

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:90759765..90760695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC1
• Ensembl ID: ENSG00000174891
• Aliases: RSRC1, SFRS21, SRrp53
• Description: arginine/serine-rich coiled-coil 1 [Source:HGNC Symbol;Acc:24152]

Sequence

>retro_hsap_4281
CACTGTAGATGGTCCTCATCGAGGAGTTCTTCAGATAGTAGAATATACAGGTGAAAGAAAGAAGGAAGGAAATCAAGATC
AAAGTCAAAATCTTGGTCCAGAGATCTTCAGCCTTATTCGCATTCTTATGATAGAAGATGCAGGCATCAACCAAGGAGTA
GCTCTCATGGCTCTAGAAGGAAACTAACTCGAAGTCGTTCAAGGGATGGAGAGAAATCCTATGGAGTTAAGAGGTCTAGG
TCAAAAAGCAGAATAAGAAGATCTAGGTCAAGGCCTTGTCTGTGTTCTCACAGTCGGAGCAGTGAAAGGTCCAGCCACAG
AAGAATGCATAGTTGGTCTCGGGATAAAGAACAACGTAAAGTCAGAGATAAAGAGAAAAGGGGAAGGATTAAGGGAAGGA
CAAGGATTACATAACATCAAATCTGGAATCTGGAAACATCAAAGCTGGATTAAACCATCTGCCACCAGCTGAAGAGGCCA
AAGCCAGAATACAGCTGGTTCTTGAAGCTGCTGCAAAAGCTGATGAAGCATTGAAATCCAAAGAAAGAAATGAGGAAGAA
GCAAAGAGAAGAAAGGAGGAAGACCACGCCACCCTGGTAGAACAAGTGAAAAAAGTGAAAGAAATGGAAGCTGTTGAAAG
TGATTCCTTTGTTCAGCAGACATTCAGATCAATTAAGAAGTCAAAAAGTTAGTGGAATCTGGTGAAGCGAAACGTGCAAC
TTCAACATCAGGACCAACATTAGCAGGTGTTGATCCACCCAGTACTGAAAACGAAATACAACTGAGCAGCATCCCTACTT
CTATCAAATACCAAGATGACAATTCCCTGGCCCATCCAAATTTATTTATAGAGAAAGCTGGTGCTGAGCAAAAATGATTC
AGAGGCTAATTGCTCTCTGACAGGAAAGACTAATGGGCAGTCCTGTGGCC

Alignment

ORF - retro_hsap_4281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.84 %
• Parental protein coverage: 94.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HRRRSSSSSSSDSRTYSRKKGGRKSRSKSRSWSRDLQPRSHSYDRRRRHRSSSSSSYGSRRKRSRSRSRG
          H.R.SSS.SSSDSR.Y..KK.GRKSRSKS.SWSRDLQP.SHSYDRR.RH...SSS..GSRRK..RSRSR.
Retrocopy HCRWSSSRSSSDSRIYR*KKEGRKSRSKSKSWSRDLQPYSHSYDRRCRHQPRSSS-HGSRRKLTRSRSRD

Parental  RGKSYRVQRSRSKSRTRRSRSRPRLRSHSRSSERSSHRRTRSRSRDRERRKGRDKEK-REKEKDKGKDKE
          ..KSY.V.RSRSKSR.RRSRSRP.L.SHSRSSERSSHRR..S.SR...........K.REK.KD.GKDK.
Retrocopy GEKSYGVKRSRSKSRIRRSRSRPCLCSHSRSSERSSHRRMHSWSR--DKEQRKVRDK<REKGKD*GKDKD

Parental  LHNIKRGESGNIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKERNEEEAKRRKEEDQATLVEQVKR
          .......ESGNIKAGL.HLPPAE.AKAR.QLVLEAAAKADEALK.KERNEEEAKRRKEED.ATLVEQVK.
Retrocopy -YITSNLESGNIKAGLNHLPPAEEAKARIQLVLEAAAKADEALKSKERNEEEAKRRKEEDHATLVEQVKK

Parental  VKEIEAIESDSFVQQTFRSSK-EVKKSVEPSEVKQATSTSGPASAVADPPSTEKEIDPTSIPTAIKYQDD
          VKE.EA.ESDSFVQQTFRS.K.EVKK.VE..E.K.ATSTSGP..A..DPPSTE.EI...SIPT.IKYQDD
Retrocopy VKEMEAVESDSFVQQTFRSIK<EVKKLVESGEAKRATSTSGPTLAGVDPPSTENEIQLSSIPTSIKYQDD

Parental  NSLAHPNLFIEKADAEEKWFK-RLIALRQERLMGSPVA
          NSLAHPNLFIEKA.AE.K.F..RLIAL.QERLMGSPVA
Retrocopy NSLAHPNLFIEKAGAEQK*FR<RLIAL*QERLMGSPVA

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	0.02 RPM	27.13 RPM
bodymap2_adrenal	0.00 RPM	28.19 RPM
bodymap2_brain	0.00 RPM	50.07 RPM
bodymap2_breast	0.00 RPM	28.07 RPM
bodymap2_colon	0.00 RPM	24.38 RPM
bodymap2_heart	0.00 RPM	14.12 RPM
bodymap2_kidney	0.00 RPM	25.77 RPM
bodymap2_liver	0.00 RPM	10.06 RPM
bodymap2_lung	0.00 RPM	12.45 RPM
bodymap2_lymph_node	0.00 RPM	25.36 RPM
bodymap2_ovary	0.00 RPM	29.40 RPM
bodymap2_prostate	0.00 RPM	26.69 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.10 RPM
bodymap2_testis	0.17 RPM	31.69 RPM
bodymap2_thyroid	0.00 RPM	32.99 RPM
bodymap2_white_blood_cells	0.00 RPM	22.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4281 was not detected

EST

No EST(s) were mapped for retro_hsap_4281 retrocopy.

TSS

No TSS is located nearby retro_hsap_4281 retrocopy 5' end.

Lab

retro_hsap_4281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4281 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004797	1 retrocopy	retro_cjac_553,
Cavia porcellus	ENSCPOG00000000876	2 retrocopies	retro_cpor_618, retro_cpor_671,
Echinops telfairi	ENSETEG00000017217	1 retrocopy	retro_etel_1555,
Homo sapiens	ENSG00000174891	1 retrocopy	retro_hsap_4281 ,
Mus musculus	ENSMUSG00000034544	1 retrocopy	retro_mmus_666,
Nomascus leucogenys	ENSNLEG00000004137	1 retrocopy	retro_nleu_2851,
Rattus norvegicus	ENSRNOG00000012639	2 retrocopies	retro_rnor_2454, retro_rnor_577,
Tupaia belangeri	ENSTBEG00000001973	13 retrocopies	retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840,