RetrogeneDB ID: retro_pabe_274

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:94439341..94440553(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSPPYG00000019140
• Aliases: None
• Description: smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:18247]

Sequence

>retro_pabe_274
CAGCCAGGGCGATATATTCATCTGCAGAACCTTTTGGCCAGGTCTTACTTTGATCCTCGTGAGGCATACCCAGATGGAAG
TAGCAAAGAAAAGAGAAGAGCAGCAATTGCCCAGGCCTTAGCTGGTGAAGTCAGTGTGGTGCCTCCATCTTATCTCATGG
CATTGCTGGGACAGGCACTGAAGTGGCAGCAGCATCAGGGATTGCTTCCTCCTGGTATGACCATAGATTTGTTTCGAGGC
AAAGCAGCTGTCAAAGATGTGGAAGAAGAAAAGTTTCCTACACAACTGAGCAGGCATATTAAGTTTGGTCAGAAATCACA
TGTGGAGTGTGCTCAATTTTCTCCAGATGGTCAGTATTTGGTCACTGGGTCTGTTGATGGATTCATTGAAGTATGGAACT
TTACTACTGGAAAAATAAGAAAGGATCTTTAGTATCAGGCCCAGGATAACTTTATGATGATGGATGATGCTGTCCTCTGC
ATGTGTTTCAGCAGAGATACAGAAATGTTAGCAACTGGTGCCCAAGATGGAAAAATCAAGGTATGGAAGATTCAGAGTAG
ACAATGTTTAAGGAGATATGAGAGGGCACACAGTAAGGGTATCACCTGTCTAAGCTTTTCTAAGGATAGCAGTCAGATCC
TTAGTGCTTCTTTTGACCAGACAATTAGAATTCACGGTTTAAAATCTGGGAAAACCCTGAAGGAATTTGGTGGCCATTCC
TCCTTTGTTAACAAAGCAACATTTACACAAGATGGACATTATATTATTAGTGCATCCACTGATGGCACTGTAAAGATCTG
GAATATGAAGACCACAGAATGTTCAAATACCGTTAAATCCCTGGGCAGCACTGCGGGGACAGATATTACCGTCAACAGTG
TGATTCCACTTCCTAAAAATCCTGAACACTTTGTGGTGTGCAACAGATCAAACACGGTGGTCATCATGAACATGCAGGGG
CAGATTGTCAGAAACTTCAGTTCTGGTAAAAGAGAAGGTAGGGACTTTGTTTGCTGTGCCCTCTCTCCCCGTGGTGAATG
GATCTACTGTGTAGGGGAGGACTTTGTGCTCTACTGTTTCAGTATAGTCACTGGCAAACTGGAGAGAACTTTGACAGTCC
AAGAGAAGGATGTGATTGGTATTGCACGTCACGCTCATCAGAACCTGATTGCTACCTACAGTGAAGATGGATTCCTCAAG
CTCTGGAAACCA

Alignment

ORF - retro_pabe_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.05 %
• Parental protein coverage: 78.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPERYIHLENLLARSYFDPREAYPDGSSKEKRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLP
          QP.RYIHL.NLLARSYFDPREAYPDGSSKEKRRAAIAQALAGEVSVVPPS.LMALLGQALKWQQHQGLLP
Retrocopy QPGRYIHLQNLLARSYFDPREAYPDGSSKEKRRAAIAQALAGEVSVVPPSYLMALLGQALKWQQHQGLLP

Parental  PGMTIDLFRGKAAVKDVEEEKFPTQLSRHIKFGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFTTGKIR
          PGMTIDLFRGKAAVKDVEEEKFPTQLSRHIKFGQKSHVECA.FSPDGQYLVTGSVDGFIEVWNFTTGKIR
Retrocopy PGMTIDLFRGKAAVKDVEEEKFPTQLSRHIKFGQKSHVECAQFSPDGQYLVTGSVDGFIEVWNFTTGKIR

Parental  KDLKYQAQDNFMMMDDAVLCMCFSRDTEMLATGAQDGKIKVWKIQSGQCLRRFERAHSKGVTCLSFSKDS
          KDL.YQAQDNFMMMDDAVLCMCFSRDTEMLATGAQDGKIKVWKIQS.QCLRR.ERAHSKG.TCLSFSKDS
Retrocopy KDL*YQAQDNFMMMDDAVLCMCFSRDTEMLATGAQDGKIKVWKIQSRQCLRRYERAHSKGITCLSFSKDS

Parental  SQILSASFDQTIRIHGLKSGKTLKEFRGHSSFVNEATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKS
          SQILSASFDQTIRIHGLKSGKTLKEF.GHSSFVN.ATFTQDGHYIISAS.DGTVKIWNMKTTECSNT.KS
Retrocopy SQILSASFDQTIRIHGLKSGKTLKEFGGHSSFVNKATFTQDGHYIISASTDGTVKIWNMKTTECSNTVKS

Parental  LGSTAGTDITVNSVILLPKNPEHFVVCNRSNTVVIMNMQGQIVRSFSSGKREGGDFVCCALSPRGEWIYC
          LGSTAGTDITVNSVI.LPKNPEHFVVCNRSNTVVIMNMQGQIVR.FSSGKREG.DFVCCALSPRGEWIYC
Retrocopy LGSTAGTDITVNSVIPLPKNPEHFVVCNRSNTVVIMNMQGQIVRNFSSGKREGRDFVCCALSPRGEWIYC

Parental  VGEDFVLYCFSTVTGKLERTLTVHEKDVIGIAHHPHQNLIATYSEDGLLKLWKP
          VGEDFVLYCFS.VTGKLERTLTV.EKDVIGIA.H.HQNLIATYSEDG.LKLWKP
Retrocopy VGEDFVLYCFSIVTGKLERTLTVQEKDVIGIARHAHQNLIATYSEDGFLKLWKP

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	20.51 RPM
SRP007412_cerebellum	0.00 RPM	28.33 RPM
SRP007412_heart	0.00 RPM	14.27 RPM
SRP007412_kidney	0.00 RPM	18.03 RPM
SRP007412_liver	0.00 RPM	18.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_274 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_274 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_457
Pan troglodytes	retro_ptro_344
Gorilla gorilla	retro_ggor_440

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006212	1 retrocopy	retro_cpor_819,
Homo sapiens	ENSG00000122692	1 retrocopy	retro_hsap_457,
Gorilla gorilla	ENSGGOG00000014802	1 retrocopy	retro_ggor_440,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,
Ochotona princeps	ENSOPRG00000011389	2 retrocopies	retro_opri_19, retro_opri_741,
Pongo abelii	ENSPPYG00000007796	1 retrocopy	retro_pabe_1932,
Pongo abelii	ENSPPYG00000014001	2 retrocopies	retro_pabe_320, retro_pabe_321,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274 ,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,