RetrogeneDB ID: retro_hsap_1745

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:30367548..30368541(+)
• Located in intron of: ENSG00000185158

Retrocopy information

• Ensembl ID: ENSG00000266777
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSG00000141985
• Aliases: SH3GL1, CNSA1, EEN, SH3D2B, SH3P8
• Description: SH3-domain GRB2-like 1 [Source:HGNC Symbol;Acc:10830]

Sequence

>retro_hsap_1745
CTTCAAAGAGATGGAGATGTCATCAGCAAGGCGGTGACGGAAATGCTGGCAAGGACCATCAAGTACCTGCAGCCCAACCC
AGCCTCACAGGCTAAGCTGACCATGCTCAACACAGTGTGCAAGATCCAGGGCCAGGTGAAGAACCCCGGCTACCCGCAGT
TGGAGGGGCTCCTGAGCGAGTGCCTGATCCGCCACCAGAAGGAGCTGGGCAACGAGTCCAACTTCAGTGACGCACTGCTG
GATGCCGGCGAGTCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACCT
CCTCCAGAACCTGTGTGAGAAAGACCTGAAGGGGATCCAGCACCACCTGCAGAAGCTGGAGGGCCGCCGCCTGGACTTTG
ACTAAAAGAAGCGGCAGGGCAAGATCCCCGATGAGGAGCTGCGTCAGGCGCTGGAGAAGTTTGAGGACTCCAAGGAGGTA
GCAGAAACCAGCATGCACAACCTCCTGGAGACCAACATTGAGCAGGTGAGTCAACTCCGGGCCCTGGCGGAGGCGCAGCT
GAACTACCACTGGCAGGCCATGCAGATCCTGGACGAGCTGGCAGAGAAGCTCAAGCGCAGGATGCGGGAAGCTTCCTCAC
GCCCCAAGCGGGAGTATAAGCCCAAGTTCTGGGAGCCCTTTGACCTCGGAGAGCCTGAGCAGTCCAATGGGGGCTTCCCC
TGCACCACAGTCCCCAAGATTGCAGCTTCATCCCCTTTCCGATCTTCCGACAAGTCCATCTGGACTCCTAGCAGGAGCAT
GCCGCCCCTAGACCAGCCAAGCTGCAAGGTGCTGTATGACTTCCAGCCTGAGAACCATGGGGAGCTGGGCTTCCATGAGG
GTGACGTCTTCACGCTGATCAACCAGATCAACGAGAACTGGTACCAGGGCATGCTGGACAGCCAGTTGGGCTTCTTCCTG
CTCAGCTACATGGACGTGCTCATGCCTCTGCCC

Alignment

ORF - retro_hsap_1745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.94 %
• Parental protein coverage: 90.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELG
          .....DV.SKAVTE.LARTI.YLQPNPAS.AKLTMLNTV.KI.GQVKNPGYPQ.EGLL.EC.IRH.KELG
Retrocopy LQRDGDVISKAVTEMLARTIKYLQPNPASQAKLTMLNTVCKIQGQVKNPGYPQLEGLLSECLIRHQKELG

Parental  GESNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQ
          .ESNF.DALLDAGESMK.LAEVKDSLDIEVKQNFID.LQNLCEKDLK.IQHHL.KLEGRRLDFD.KK.RQ
Retrocopy NESNFSDALLDAGESMKHLAEVKDSLDIEVKQNFIDLLQNLCEKDLKGIQHHLQKLEGRRLDFD*KK-RQ

Parental  GKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMR
          GKIPDEELRQALEKFE.SKEVAETSMHNLLET.IEQVSQL.AL..AQL.YH.QA.QILDELAEKLKRRMR
Retrocopy GKIPDEELRQALEKFEDSKEVAETSMHNLLETNIEQVSQLRALAEAQLNYHWQAMQILDELAEKLKRRMR

Parental  EASSRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALY
          EASSRPKREYKPK..EPFDLGEPEQSNGGFPCTT.PKIAASS.FRSSDK.I.TPSRSMPPLDQPSCK.LY
Retrocopy EASSRPKREYKPKFWEPFDLGEPEQSNGGFPCTTVPKIAASSPFRSSDKSIWTPSRSMPPLDQPSCKVLY

Parental  DFEPENDGELGFHEGDVITLTNQIDENWYEGMLDGQSGFFPLSYVEVLVPLP
          DF.PEN.GELGFHEGDV.TL.NQI.ENWY.GMLD.Q.GFF.LSY..VL.PLP
Retrocopy DFQPENHGELGFHEGDVFTLINQINENWYQGMLDSQLGFFLLSYMDVLMPLP

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	0.16 RPM	61.30 RPM
bodymap2_adrenal	0.29 RPM	44.54 RPM
bodymap2_brain	0.07 RPM	14.81 RPM
bodymap2_breast	0.23 RPM	32.30 RPM
bodymap2_colon	0.08 RPM	39.72 RPM
bodymap2_heart	0.07 RPM	7.38 RPM
bodymap2_kidney	0.08 RPM	19.61 RPM
bodymap2_liver	0.00 RPM	12.63 RPM
bodymap2_lung	0.26 RPM	33.98 RPM
bodymap2_lymph_node	0.84 RPM	28.95 RPM
bodymap2_ovary	0.15 RPM	59.89 RPM
bodymap2_prostate	0.19 RPM	36.20 RPM
bodymap2_skeletal_muscle	0.16 RPM	12.70 RPM
bodymap2_testis	0.25 RPM	41.36 RPM
bodymap2_thyroid	0.00 RPM	31.96 RPM
bodymap2_white_blood_cells	0.08 RPM	20.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1745 was not detected

EST

No EST(s) were mapped for retro_hsap_1745 retrocopy.

TSS

No TSS is located nearby retro_hsap_1745 retrocopy 5' end.

Lab

retro_hsap_1745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1745 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000141985	3 retrocopies	retro_hsap_1742, retro_hsap_1745 , retro_hsap_1859,
Gorilla gorilla	ENSGGOG00000008198	3 retrocopies	retro_ggor_2151, retro_ggor_2258, retro_ggor_675,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Monodelphis domestica	ENSMODG00000000931	1 retrocopy	retro_mdom_1530,
Nomascus leucogenys	ENSNLEG00000003122	2 retrocopies	retro_nleu_2914, retro_nleu_3075,
Pongo abelii	ENSPPYG00000009405	6 retrocopies	retro_pabe_1488, retro_pabe_1516, retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.23 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.34 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.12 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.26 RPM
GBR_HG00137	0.14 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.19 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.44 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	0.23 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.08 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.30 RPM
YRI_NA18907	0.21 RPM
YRI_NA18916	0.17 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.22 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.24 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).