RetrogeneDB ID: retro_pabe_315

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:164403934..164405172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC2A3
• Ensembl ID: ENSPPYG00000004235
• Aliases: SLC2A3, GLUT3
• Description: solute carrier family 2, facilitated glucose transporter member 3 [Source:RefSeq peptide;Acc:NP_001127589]

Sequence

>retro_pabe_315
TTTGTCAACAGCTTTGACAGGCGTAATTCAATGCTTACTGTCAATCTGTTGGCTGTCACTGGTGGCTGCCTTGTGGGATT
GTGTAAAGTAGCTGAGTTGGTTGAAATACTGATCCTGGCCTACTTGGTTATTGGCCTCTTCTGCAGACTCTGCACAGGTT
TTGTGCCCACATACATCGGAGAGATCTCACCTGTTGCCCTGCAAGGTGTCTTTGGCACTCTCAACCAGCTGGGCATTGTT
GTTGGAATTCTGGTGGCCCAGATCTTTGATCTGGAATTCATCCTGGGGTCTGAAGACCTATGGCCTGTGCTATTAGGCTT
TCCCATCTCTCCTGCTATGCTACAAAGTGCAGCCCTTCCTTTTTGCCCTGAAAGTCCCAGATTCTTGCTCATTAACAGAA
AAGAAGAGGAGAATGCTAAGGAGATCCTCCAGTGGTTGTGGGGCACCCAGAATGTATCCCAAGACATCCAGGAGATGAAA
GATGAGAGTGCAAGGATGGCACAAGAAAAGCAAGTCACTGTGCTGGAGCTCTTTAGAGTATCCAGCTACCAACAGCCCAT
CATCATTTCCATCATGCTCCAGCTCTCTCAGCAGCTCTCTGGAATCAATGCTGTGTTCTGTTACTCAACAGGAATCTTTA
AGGGTGCAGGTGTTCAAGAGCCCATCTGTGTCACCATCGGTGCGGGTGTGGTTAATACTATCTTCACTATAGTTTCCCTA
TTTCTGGTGGAAAGGGCAGTAAGAAGGACTCTACATATGATAGGCCTTGGAGGGATGACTTTTTGTTCCATCCTCATGAC
TGTTTGTTTGTTATTGAAGGCTGAGTGTAATGGGATAAGCTTTGTCTGTATTGGGGCTATCTTGGTCTTTGTGGTCTTCT
TTGAAATTGGGCCAGGCCCCATTCCCTGGTTTATTGTGGCTGAACTCTTCAGCCAGGGCCCTGGCCCAGCTGTGATGGCA
GTGGCCGGCTGCTCCAACTGGACCTCCAACTTCCTAGTCAGATTGCTCTTCCCTTCTGCTGCTTACCATTTAGGAGCCTA
CGTTTTTATTATCTTCACTGACTTCCTCATTACCTTCTCGATCTTTACCTTCTTCAAAGTCCCTGAGATGTGTTACAGGA
CTTTCGAGGATATCACACAGGCCTTTGAGGGGCAGGCACACGATGCAAATAGATCTGGAAGGACCGCGTCATGGAGATGA
ACAGTATCCAGCCTGCTAAGGAGACCACCACCAATGTC

Alignment

ORF - retro_pabe_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 97.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FVNRFGRRNSMLIVNLLAVTGGCFMGLCKVAKSVEMLILGRLIIGLFCGLCTGFVPMYIGEISPTALRGA
          FVN.F.RRNSML.VNLLAVTGGC..GLCKVA..VE.LIL..L.IGLFC.LCTGFVP.YIGEISP.AL.G.
Retrocopy FVNSFDRRNSMLTVNLLAVTGGCLVGLCKVAELVEILILAYLVIGLFCRLCTGFVPTYIGEISPVALQGV

Parental  FGTLNQLGIVVGILVAQIFGLEFILGSEELWPLLLGFTILPTILQSAALPFCPESPRFLLINRKEEENAK
          FGTLNQLGIVVGILVAQIF.LEFILGSE.LWP.LLGF.I.P..LQSAALPFCPESPRFLLINRKEEENAK
Retrocopy FGTLNQLGIVVGILVAQIFDLEFILGSEDLWPVLLGFPISPAMLQSAALPFCPESPRFLLINRKEEENAK

Parental  QILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQLSGINAVFYYST
          .ILQ.LWGTQ.VSQDIQEMKDESARM.QEKQVTVLELFRVSSY.QPIIISI.LQLSQQLSGINAVF.YST
Retrocopy EILQWLWGTQNVSQDIQEMKDESARMAQEKQVTVLELFRVSSYQQPIIISIMLQLSQQLSGINAVFCYST

Parental  GIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTVSLLLKDNYNGMS
          GIFK.AGVQEPI..TIGAGVVNTIFT.VSLFLVERA.RRTLHMIGLGGM.FCS.LMTV.LLLK...NG.S
Retrocopy GIFKGAGVQEPICVTIGAGVVNTIFTIVSLFLVERAVRRTLHMIGLGGMTFCSILMTVCLLLKAECNGIS

Parental  FVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFPSAAHYLGAYVFI
          FVCIGAILVFV.FFEIGPGPIPWFIVAELFSQGP.PA.MAVAGCSNWTSNFLV.LLFPSAA..LGAYVFI
Retrocopy FVCIGAILVFVVFFEIGPGPIPWFIVAELFSQGPGPAVMAVAGCSNWTSNFLVRLLFPSAAYHLGAYVFI

Parental  IFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQAHGADRSG-KDGVMEMNSIEPAKETTTNV
          IFT.FLITF..FTFFKVPE...RTFEDIT.AFEGQAH.A.RSG.KD.VMEMNSI.PAKETTTNV
Retrocopy IFTDFLITFSIFTFFKVPEMCYRTFEDITQAFEGQAHDANRSG<KDRVMEMNSIQPAKETTTNV

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	0.11 RPM	116.72 RPM
SRP007412_cerebellum	0.00 RPM	103.73 RPM
SRP007412_heart	0.06 RPM	47.62 RPM
SRP007412_kidney	0.07 RPM	36.76 RPM
SRP007412_liver	0.09 RPM	113.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_315 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_315 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_401
Pan troglodytes	retro_ptro_307
Gorilla gorilla	retro_ggor_398
Macaca mulatta	retro_mmul_502

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 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,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
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,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315 ,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,