RetrogeneDB ID: retro_ptro_739

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:15546016..15546711(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL8
• Ensembl ID: ENSPTRG00000012630
• Aliases: None
• Description: None

Sequence

>retro_ptro_739
TCCAACCTAGACTCTGAAAAACACAAAAAAGGACGTATGAAGACCGATTGTTTCCTGGTAGCAGTGCCACTTTCAGGATA
CTAGAGGTTGGTTGTGGAGTTGGAAATAGTGTGTTTCCAATTTTGAACACTTTGCAGAGCTTTCCAGAGTCCTTTCTGTA
TTGTTGTGATTTTGCTTCTGGAGCTGTGGAGCTCGTAAAGTCACACTCGTCCTACAGAGCAGCCCAGTGTTTTGCCTTTG
TTCATGATGTATGTGATGATGGCTTACCTTACCCTTTTCCAGATGGGATCCTAGATGTCATTCTCCTTGTCTTTGTGCTC
TCTTCTATTCATCCTAACAGGATGCAAGGTGTTGTAAACCTACTGTCCAAGCTACTGAAACCTGGGGGAATGCTGTTATT
TTGAGACTATGGAAGATATAAGACTCAGCTTCGTTTTAAAAAGGGACATTGTTTATCTGAAAATTTTTATGTTCGAGGAG
ATGGTACCAGAGCATATTTCTTTACAAAAGGGGAAGTCCACAGTATGTTCTGCAAAGCCAGTTTAGATGAAAAGCAAAAT
CCGGTTGATTGCCGCTTACAAGTTAATAGGAAAAAACAAGTAAAAATGCACCGAGTGTGGGTTCAAGGCAAATTCCAGAA
ACCATTGCACCAGACTCAGAATACTTCCAATATGGTATCTACACTCCTTTCTCAA

Alignment

ORF - retro_ptro_739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SNLDSEKHKKGPMETG-LFPGSNATFRILEVGCGAGNSVFPILNTLQNSPESFLYCCDFASGAVELVKSH
          SNLDSEKHKKG.M.T..LFPGS.ATFRILEVGCG.GNSVFPILNTLQ..PESFLYCCDFASGAVELVKSH
Retrocopy SNLDSEKHKKGRMKTD<LFPGSSATFRILEVGCGVGNSVFPILNTLQSFPESFLYCCDFASGAVELVKSH

Parental  SSYRATQCFAFVHDVCDDGLPYPFPDGILDVILLVFVLSSIHPDRMQGVVNRLSKLLKPGGMLLFRDYGR
          SSYRA.QCFAFVHDVCDDGLPYPFPDGILDVILLVFVLSSIHP.RMQGVVN.LSKLLKPGGMLLF.DYGR
Retrocopy SSYRAAQCFAFVHDVCDDGLPYPFPDGILDVILLVFVLSSIHPNRMQGVVNLLSKLLKPGGMLLF*DYGR

Parental  YDKTQLRFKKGHCLSENFYVRGDGTRAYFFTKGEVHSMFCKASLDEKQNLVDRRLQVNRKKQVKMHRVWI
          Y.KTQLRFKKGHCLSENFYVRGDGTRAYFFTKGEVHSMFCKASLDEKQN.VD.RLQVNRKKQVKMHRVW.
Retrocopy Y-KTQLRFKKGHCLSENFYVRGDGTRAYFFTKGEVHSMFCKASLDEKQNPVDCRLQVNRKKQVKMHRVWV

Parental  QGKFQKPLHQTQNSSDMVSTLLSQ
          QGKFQKPLHQTQN.S.MVSTLLSQ
Retrocopy QGKFQKPLHQTQNTSNMVSTLLSQ

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	0.77 RPM
SRP007412_cerebellum	0.00 RPM	0.68 RPM
SRP007412_heart	0.00 RPM	1.40 RPM
SRP007412_kidney	0.00 RPM	2.22 RPM
SRP007412_liver	0.00 RPM	1.73 RPM
SRP007412_testis	0.00 RPM	1.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_739 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_739 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1087
Pongo abelii	retro_pabe_905

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013075	1 retrocopy	retro_dord_87,
Homo sapiens	ENSG00000123600	1 retrocopy	retro_hsap_1087,
Nomascus leucogenys	ENSNLEG00000005370	1 retrocopy	retro_nleu_1622,
Pongo abelii	ENSPPYG00000012927	1 retrocopy	retro_pabe_905,
Pan troglodytes	ENSPTRG00000012630	1 retrocopy	retro_ptro_739 ,