RetrogeneDB ID: retro_ptro_2266

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:59272340..59273428(-)
• Located in intron of: ENSPTRG00000016888

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1GALT1
• Ensembl ID: ENSPTRG00000018925
• Aliases: None
• Description: None

Sequence

>retro_ptro_2266
ATGGCCTCTAAATCCTGGCTGAATTTTTTAACCTTCCTCTGTGGATCGGCAATAGGGTTTATTTTATTTTCTCAGCTACT
TAGTATTTTGTTGGGAGAAGAGGGTGACACCCAGACTAATGTTCTTCATAATGATCCTCATGCGAGGCATTCAGATGATA
ATGGACAGAATCATCTAGAAGGACAAATGAACTTCAATGCAGATTCTAGCCAACGCAAAGATGAGAACATAGACATCGCT
GAAAACATCTATTAGCAAGTTAAAATTCTTTGCTGGGTTATGACAGGCTCTCAAAACCTAGAGAAAAAGGCCAATCATGT
CAAAGCTACATGGGCCCAGCGTTGTCTAAAAGTATTTTTTATGAGTTCAGAAGAAAATAAAGACTTTCCTGCTGTGGGAT
TGAAAACCAAAGAAGGCAGAGATGAGCTATACTGGAAAACAATTAAACCTTTTCAGTATGTTCATGAACATCATTTAGAA
GATGCTGATTGTTTTTTGAAAGCAGATGATGACACATATTTCATACTAGATAATTTGAGATGGCTTCTTTCAAAATATGA
TTCTAAAGAACCCATTTATTTTAGGAGAAGATTTAAGCCCTTTGTAAAACAGGGCTGTATGAGTGGAGGAGCAGGATATT
TACTAAGCAAAGAAAGCCTTGAAAAGATTTCTTGATGCATTTAAAACAGACAAGTGTCACGTAGTTCCTCCACTGAAGAC
TTAGCACTGGGGAGATGCATGGAAATTATAAATGTAGAAGCAGGAGATTCCAGAGATCCAACTGGAAAAGAAACTTTTCA
TCCCTTTGTTTCAGAACACCATTTAATAAAGGTTATCTACCTAGAACCTTTTGGTACTGGAATTACAACTATTATCCTCC
TGTAGAGGGTCCTGGTTGCTGTTCCGATCTTGCAGTTTCTTTTCACTATGTTGATTTTACAACTGTGTATGTGTTAGAAT
ACCTCGTTTATCATCTTCATCCATATGGTTATTTATACAGATATCAAGCTACCTTACCTGAAAATATACTAAAGGAAATT
AGTCAAGCAAACAAAAATGAAGGCACAAAAGTGAAGTCAGGAAACCCT

Alignment

ORF - retro_ptro_2266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASKSWLNFLTFLCGSAIGFLLCSQLFSILLGEKGDTQPNVLHNDPHARHSDDNGQNHLEGQMNFNADSS
          MASKSWLNFLTFLCGSAIGF.L.SQL.SILLGE.GDTQ.NVLHNDPHARHSDDNGQNHLEGQMNFNADSS
Retrocopy MASKSWLNFLTFLCGSAIGFILFSQLLSILLGEEGDTQTNVLHNDPHARHSDDNGQNHLEGQMNFNADSS

Parental  QHKDENTDIAENLYHKVRILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPAVGLKTKEGR
          Q.KDEN.DIAEN.Y..V.ILCWVMTG.QNLEKKA.HVKATWAQRC.KV.FMSSEENKDFPAVGLKTKEGR
Retrocopy QRKDENIDIAENIY*QVKILCWVMTGSQNLEKKANHVKATWAQRCLKVFFMSSEENKDFPAVGLKTKEGR

Parental  DQLYWKTIKAFQYVHEHYLEDADWFLKADDDTYVILDNLRWLLSKYDPEEPIYFGRRFKPYVKQGYMSGG
          D.LYWKTIK.FQYVHEH.LEDAD.FLKADDDTY.ILDNLRWLLSKYD..EPIYF.RRFKP.VKQG.MSGG
Retrocopy DELYWKTIKPFQYVHEHHLEDADCFLKADDDTYFILDNLRWLLSKYDSKEPIYFRRRFKPFVKQGCMSGG

Parental  AGYVLSKE-ALKRFVDAFKTDKC-THSSSIEDLALGRCMEIMNVEAGDSRDTIGKETFHPFVPEHHLI-K
          AGY.LSKE.ALKRF.DAFKTDKC...SSS.EDLALGRCMEI.NVEAGDSRD..GKETFHPFV.EHHLI.K
Retrocopy AGYLLSKE>ALKRFLDAFKTDKC<SRSSSTEDLALGRCMEIINVEAGDSRDPTGKETFHPFVSEHHLI<K

Parental  GYLPRTFWYWNYNYYPPVEGPGCCSDLAVSFHYVDSTTMYELEYLVYHLRPYGYLYRYQPTLPEHILKEI
          GYLPRTFWYWNYNYYPPVEGPGCCSDLAVSFHYVD.TT.Y.LEYLVYHL.PYGYLYRYQ.TLPE.ILKEI
Retrocopy GYLPRTFWYWNYNYYPPVEGPGCCSDLAVSFHYVDFTTVYVLEYLVYHLHPYGYLYRYQATLPENILKEI

Parental  SQANKNEDTKVKLGNP
          SQANKNE.TKVK.GNP
Retrocopy SQANKNEGTKVKSGNP

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	0.02 RPM	3.52 RPM
SRP007412_cerebellum	0.00 RPM	3.01 RPM
SRP007412_heart	0.00 RPM	4.84 RPM
SRP007412_kidney	0.03 RPM	10.41 RPM
SRP007412_liver	0.00 RPM	3.11 RPM
SRP007412_testis	0.00 RPM	2.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2266 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2266 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3177
Macaca mulatta	retro_mmul_2009

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000225	2 retrocopies	retro_chof_1782, retro_chof_2581,
Dasypus novemcinctus	ENSDNOG00000017353	2 retrocopies	retro_dnov_1801, retro_dnov_1905,
Homo sapiens	ENSG00000106392	2 retrocopies	retro_hsap_3177, retro_hsap_4065,
Loxodonta africana	ENSLAFG00000000063	1 retrocopy	retro_lafr_1166,
Myotis lucifugus	ENSMLUG00000014789	1 retrocopy	retro_mluc_1310,
Macaca mulatta	ENSMMUG00000016338	1 retrocopy	retro_mmul_2009,
Oryctolagus cuniculus	ENSOCUG00000026002	1 retrocopy	retro_ocun_216,
Otolemur garnettii	ENSOGAG00000012847	1 retrocopy	retro_ogar_855,
Petromyzon marinus	ENSPMAG00000001562	1 retrocopy	retro_pmar_2,
Pan troglodytes	ENSPTRG00000018925	2 retrocopies	retro_ptro_2266 , retro_ptro_2755,