RetrogeneDB ID: retro_ptro_2755

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:59651901..59652836(-)
• Located in intron of: None

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_2755
ATTAATAATTATTCTTACGTGAGGCCTTCAGATGATACTGGACAGAATCATCTAAAAAGACTGATGAAGTTGATTGCAAA
TGCTAGTCATGATAAATACCAGAACACAGGTGTCACTGACAAACTCTATCAAAAGATGAAAATTCTTTGCTGGATAATGA
CAGGACCTCAAAATCTAGAAAAAAAAGGTCATACACATCAGAGATACAGGGGCCCAGGGTTGCAATAAAGCGTTGTTTAT
GAGCTCAAAAGAAAATAAAGGCTTCTCTACTGTGGGATTACACACCAAAGAAGACAGAAACCAACTGTCCTGGAAAATAG
TTAAAGCTTTTCAGTACGCTCATGACCATTATCTGGAATACATGGATTGGTTCATGAAAGCAGATGATGATATATGTATA
TATACCATACTGGACAACTTGAAATGGCTTCTCACAAACTATAACCCTGATGAATCCACTTACTTTGGGAAAAGATTTAA
GCACTGCAGAAAACAGGACTACATGACTGGAGGAGCAGGATATGTACTGAGCAAAGAAGCCTCAAGGAGATTAATTGATG
TGGTCAAAACAAAAACGGGCACACCTGTGTCCTTCTCTGAATACATGGCACTGGGGAGATGCATGGACGTTGTAAAGGTG
GAACCAGAGGATTCCAGATATCACACTGGAAAAGAGACTTTTCATCCCTTTTTAGCAAAACAGCCATTAATTACAGGTTT
TCTACTAGAACCTTTTGTACTGGAAATATAACTATTATCCTTCTGTAGAGGATCCCAGTTGCTGTTCTGATTTTGCCATT
TCTTTTTACTATGTTGATGCTACAGCTATATATGGGTTAGAATATCTCATTTATCATCTTTATCTTTATGGTTATTTATA
CAGATATCAACCTGCCTTACCTGAGGATCTGTTAAAGGAAATAAGCAAAGCAAAC

Alignment

ORF - retro_ptro_2755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 85.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LHNDPHARHSDDNGQNHLEGQMNFNADSSQHKDENTDIAENLYHKVRILCWVMTGPQNLEKKAK-HVKAT
          ..N....R.SDD.GQNHL...M...A..S..K..NT.....LY.K..ILCW.MTGPQNL......H...T
Retrocopy INNYSYVRPSDDTGQNHLKRLMKLIANASHDKYQNTGVTDKLYQKMKILCWIMTGPQNLXXXGH>HIRDT

Parental  WAQRCNKVLFMSSEENKDFPAVGLKTKEGRDQLYWKTIKAFQYVHEHYLEDADWFLKADDDT--YVILDN
          .AQ.CNK.LFMSS.ENK.F..VGL.TKE.R.QL.WK..KAFQY.H.HYLE..DWF.KADDD...Y.ILDN
Retrocopy GAQGCNKALFMSSKENKGFSTVGLHTKEDRNQLSWKIVKAFQYAHDHYLEYMDWFMKADDDICIYTILDN

Parental  LRWLLSKYDPEEPIYFGRRFKPYVKQGYMSGGAGYVLSKEALKRFVDAFKTDKCTHSSSIEDLALGRCME
          L.WLL..Y.P.E..YFG.RFK...KQ.YM.GGAGYVLSKEA..R..D..KT...T..S..E..ALGRCM.
Retrocopy LKWLLTNYNPDESTYFGKRFKHCRKQDYMTGGAGYVLSKEASRRLIDVVKTKTGTPVSFSEYMALGRCMD

Parental  IMNVEAGDSRDTIGKETFHPFVPEHHLIKGYL-PRTF-WYWNYNYYPPVEGPGCCSDLAVSFHYVDSTTM
          ...VE..DSR...GKETFHPF.....LI.G.L..RTF..YW.YNYYP.VE.P.CCSD.A.SF.YVD.T..
Retrocopy VVKVEPEDSRYHTGKETFHPFLAKQPLITGFL<TRTF<LYWKYNYYPSVEDPSCCSDFAISFYYVDATAI

Parental  YELEYLVYHLRPYGYLYRYQPTLPEHILKEISQAN
          Y.LEYL.YHL..YGYLYRYQP.LPE..LKEIS.AN
Retrocopy YGLEYLIYHLYLYGYLYRYQPALPEDLLKEISKAN

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	0.00 RPM	3.52 RPM
SRP007412_cerebellum	0.00 RPM	3.01 RPM
SRP007412_heart	0.00 RPM	4.84 RPM
SRP007412_kidney	0.00 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_2755 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2755 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2755 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4065

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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 ,