RetrogeneDB ID: retro_ptro_2703

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:84605885..84606935(+)
• Located in intron of: ENSPTRG00000020396

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC2A14
• Ensembl ID: ENSPTRG00000004624
• Aliases: None
• Description: solute carrier family 2 (facilitated glucose transporter), member 14 [Source:HGNC Symbol;Acc:18301]

Sequence

>retro_ptro_2703
AAGGTCACCCCAGCTCTGATCGCTGCCATTACAGTTGCTACAATCGGCTCTTTCCAAGTTGGCTACAACACTGGGGTCAT
CAGTGCTCCTGAGATGATCATAAAGGAATTTATCAATAACACTTTGAGTGACCAGGCAAATATCCCTCACTCTCAGATGT
TGCTCACGTCCCTCTGGTCCTTGTCTGTGGCCATATTCTCCATTGTTGGTATGACTGGCTCCTTTTCCGTTAGACTCTTT
ATCAACCACTTCTTGACAGGTGCAATTCAATGCTTATCGTCAACCTGTTGGCTGTCTCTGGTGGCTGCCTTATGGGATTG
TGTAAAGTAGCTGAGTTGGTTGAAATGCTGATCCTGGGCTGCTTGGTTATTGGCCTCTTCTGTGGACTGTGCACAGGTTT
TATGCCCATGTACATTGGAGAGATCTCACCTACTGCCCTGCAGGGTACCTTTGGCACTCTCAACCAGCTGGGCATCATTG
TCAGAATTCTGGTGGCCCAGATCTTTGGTCTGGAATTCAAATTCATCCTTGGGTCTGAAGAGCTATGGCCGGTACTATTG
GGCTTTACCATCCTTCCTGCTATCCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGGTTTTTGCTCATTAA
CAGAAAAGAAGAGGAGAATGCTAAGTAGATCCTCCAGTAGTTGTGGGGCACCCAGGATGTATCCCAAGACAACCAGGAGA
TGCAAGATGAGAGTGCAAGGATGTCACAAGAAAAGCAAGTCACCATGCTGGAGTTCTTTAGAGTATCCAGCTACCAACAG
CCAATCATCACTTCCATTGTGCTCCAGCTCTCTCGACAGCTCTCTGGAATCAATGTTGTGTTCTATTACTCAACAGGAAT
CTTCAAGGATGCAGGTGTTCAAGAGCCCATCTATGCCACCATTGGTGCAGGTGTGTTTTAATACTATCTTCACTGTAGTT
TCCCTATTTCTGCTGGAAACGGCAGGAAGGCGGACCCTGCATATGATAGGCCTTGGAGGGATGGCTTTTTGTTCCATGCT
CATGACTGTT

Alignment

ORF - retro_ptro_2703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.97 %
• Parental protein coverage: 69.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVTPALIFAIAVATIGSFQFGYNTGVINAPETIIKEFINKTLTDKANAPPSEVLLTNLWSLSVAIFSIGG
          .VTPALI.AI.VATIGSFQ.GYNTGVI.APE.IIKEFIN.TL.D.AN.P.S..LLT.LWSLSVAIFSI.G
Retrocopy KVTPALIAAITVATIGSFQVGYNTGVISAPEMIIKEFINNTLSDQANIPHSQMLLTSLWSLSVAIFSIVG

Parental  MIGSFSVGLFVNRFGR-RNSMLIVNLLAATGG-CLMGLCKIAESVEMLILGRLVIGLFCGLCTGFVPMYI
          M.GSFSV.LF.N.F...R........L.A..G.CLMGLCK.AE.VEMLILG.LVIGLFCGLCTGF.PMYI
Retrocopy MTGSFSVRLFINHFLT<RCNSMLIVNLLAVSGGCLMGLCKVAELVEMLILGCLVIGLFCGLCTGFMPMYI

Parental  GEISPTALRGAFGTLNQLGIVIGILVAQIFGLE--LILGSEELWPVLLGFTILPAILQSAALPCCPESPR
          GEISPTAL.G.FGTLNQLGI...ILVAQIFGLE...ILGSEELWPVLLGFTILPAILQSAALP.CPESPR
Retrocopy GEISPTALQGTFGTLNQLGIIVRILVAQIFGLEFKFILGSEELWPVLLGFTILPAILQSAALPFCPESPR

Parental  FLLINRKKEENATRILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQ
          FLLINRK.EENA..ILQ.LWGTQDVSQD.QEM.DESARMSQEKQVT.LE.FRVSSY.QPII.SIVLQLS.
Retrocopy FLLINRKEEENAK*ILQ*LWGTQDVSQDNQEMQDESARMSQEKQVTMLEFFRVSSYQQPIITSIVLQLSR

Parental  QLSGINAVFYYSTGIFKDAGVQQPIYATISAGV-VNTIFTLVSLFLVERAGRRTLHMIGLGGMAFCSTLM
          QLSGIN.VFYYSTGIFKDAGVQ.PIYATI.AGV..NTIFT.VSLFL.E.AGRRTLHMIGLGGMAFCS.LM
Retrocopy QLSGINVVFYYSTGIFKDAGVQEPIYATIGAGV>FNTIFTVVSLFLLETAGRRTLHMIGLGGMAFCSMLM

Parental  TV
          TV
Retrocopy TV

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
SRP007412_brain_prefrontal_cortex	0.05 RPM	1.84 RPM
SRP007412_cerebellum	0.11 RPM	0.11 RPM
SRP007412_heart	0.12 RPM	0.20 RPM
SRP007412_kidney	0.10 RPM	0.31 RPM
SRP007412_liver	0.03 RPM	0.13 RPM
SRP007412_testis	0.21 RPM	469.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2703 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2703 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3983
Pongo abelii	retro_pabe_3274
Macaca mulatta	retro_mmul_2301

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703 ,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,