RetrogeneDB ID: retro_ggor_440

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:136070224..136071759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSGGOG00000014802
• Aliases: None
• Description: None

Sequence

>retro_ggor_440
ATGTTGATCAAAATTGAATCTTCGGATGTGATCCACCTTATCATGCAGTACTTGAAGGAGAACGGTTTACATCGGGCATT
AGCCACCTTGCAGGAGGAGACTATTCTGTCTCTGAATACTGTGGACAGCATTGAGAGTTTTGTGGCTGACATTAACAGTG
GCCATTGGGATACTGTGTTGCAGGCTATACAGTCTCTGAAATTGCCAGACAAAACCCTCATTGACCTCTATGAACAGATT
GTTCTGGAATTGATAGAGCTCCGTGAATTGGGTGCTGCCAGGTCACTATTGAGACAGACTGATCCCATGATCATGTTAAA
ACAAACACAGCCAGAGCAATATATTCATCTGGAGAACCTTTTGGCCAGGTCTTACTTTGATCCTCGTGAGGCATACCCAG
ATGGAAGTAGCAAAGAAAAGAGAAGAGCAGCAATTGCCCAGGCCTTAGCTGGTGAAGTCAGTGTGGTGCCTCCATCTCAT
CTCATGGCACTGCTGGGACAGGCACTGAAGTGGCAGCAGCATCAGGGATTGCTTCCTCCTGGTATGACCATAGATTTGTT
TTGAGGCAAAGCAGCTGTCAAAGATGTGGAAGAAGAAAAGTTTCCTACACAACTGAGCAGGCATATTAAGTTTGGTCAGA
AATCACAAGTGGAGTGTGCTCGATTTTCTCCAGATGGTCACTATTTGGTCACTGGGTCTGTTGATGGACTCACTGAAGTA
TGGAACTTTACTACTGGAAAAATCAGAAAGGATCTTAAGTACCAGGCCCAGGATAACTTTATGATGATGGATGATGCTGT
CCTCTGCATGTGTTTCAGCAGAGATACAGAAATGTTAGCAACTGGGGCCCAAGATGGAAAAATCAAGGTATGGAAGATTC
AGAGTAGACAATATTTAAGGAAATATGAGAGGGCACACAGTAAGGGTGTCACGTGTCTAAGCTTTTCTAAGGATAGCAGT
CAGATCCTTAGTGCTTCTTTTGACCACACAATTAGAATTCATGGTTTAAAATCTGGGAAAACCCTGAAGGAATTTTGTAG
CCATTCCTCCTTTGTTAACAAAGCAACATTTACACAAGATGGACATTATATTATTAGTGCATCCTCTGATGGCACTGTAA
AGATCTGGAATATGAAGACCACAGAATGTTCAAATACCTTTAAATCCCTGGGCAGCACTGCAGGGACAGATATTACCGTC
AACAGTGTGATTCTACTTCCTAAAAATCCTGAGCACTTTGTGGTGTGCAACAGATCAAACACAGTGGTCATCATGAACAT
GCAGGGGCAGATTGTCAGAAACTTCAGTTCTGGTAAAAGAGAAGGTGGGGACTTTTCTGTGCCCTCTCTCCCCGTGGTGA
ATGGATCTACTGTGTAGGGGAGGACTTTGTGCTCTACTGTTTCAGTACAGCCACTGGCAAACTGGAGAGAACTTTGACAG
TGCACGAGAAGGATGTGATTGGTATTGCACATCACCCTCATCAGAACCTGATTGCTACCTACAGTGAAGATGGACTCCTA
AAGCTCTGGAAACCA

Alignment

ORF - retro_ggor_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD
          M.I.IESSDVI.LIMQYLKEN.LHRALATLQEET..SLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD
Retrocopy MLIKIESSDVIHLIMQYLKENGLHRALATLQEETILSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD

Parental  KTLIDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENLLARSYFDPREAYPDGSSKEK
          KTLIDLYEQ.VLELIELRELGAARSLLRQTDPMIMLKQTQPE.YIHLENLLARSYFDPREAYPDGSSKEK
Retrocopy KTLIDLYEQIVLELIELRELGAARSLLRQTDPMIMLKQTQPEQYIHLENLLARSYFDPREAYPDGSSKEK

Parental  RRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPTQLSRHIK
          RRAAIAQALAGEVSVVPPS.LMALLGQALKWQQHQGLLPPGMTIDLF.GKAAVKDVEEEKFPTQLSRHIK
Retrocopy RRAAIAQALAGEVSVVPPSHLMALLGQALKWQQHQGLLPPGMTIDLF*GKAAVKDVEEEKFPTQLSRHIK

Parental  FGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLA
          FGQKS.VECARFSPDG.YLVTGSVDG..EVWNFTTGKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLA
Retrocopy FGQKSQVECARFSPDGHYLVTGSVDGLTEVWNFTTGKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLA

Parental  TGAQDGKIKIKVWKIQSGQCLRRFERAHSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGKTLKEFRGH
          TGAQDGKIK..VWKIQS.Q.LR..ERAHSKGVTCLSFSKDSSQILSASFD.TIRIHGLKSGKTLKEF..H
Retrocopy TGAQDGKIK--VWKIQSRQYLRKYERAHSKGVTCLSFSKDSSQILSASFDHTIRIHGLKSGKTLKEFCSH

Parental  SSFVNEATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNR
          SSFVN.ATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNR
Retrocopy SSFVNKATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNR

Parental  SNTVVIMNMQGQIVRSFSSGKREGGDF-VCCALSPRGEWIYCVGEDFVLYCFSTVTGKLERTLTVHEKDV
          SNTVVIMNMQGQIVR.FSSGKREGGDF..C.ALSPRGEWIYCVGEDFVLYCFST.TGKLERTLTVHEKDV
Retrocopy SNTVVIMNMQGQIVRNFSSGKREGGDF<FC-ALSPRGEWIYCVGEDFVLYCFSTATGKLERTLTVHEKDV

Parental  IGIAHHPHQNLIATYSEDGLLKLWKP
          IGIAHHPHQNLIATYSEDGLLKLWKP
Retrocopy IGIAHHPHQNLIATYSEDGLLKLWKP

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	0.24 RPM	25.03 RPM
SRP007412_cerebellum	0.08 RPM	21.71 RPM
SRP007412_heart	0.03 RPM	7.00 RPM
SRP007412_kidney	0.04 RPM	19.46 RPM
SRP007412_liver	0.13 RPM	14.90 RPM
SRP007412_testis	0.10 RPM	34.91 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_440 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_457
Pan troglodytes	retro_ptro_344
Pongo abelii	retro_pabe_274

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 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	ENSGGOG00000004997	2 retrocopies	retro_ggor_171, retro_ggor_2023,
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	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344,