RetrogeneDB ID: retro_pabe_979

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12_random:11029518..11030701(-)
• Located in intron of: ENSPPYG00000005175

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF1IP
• Ensembl ID: ENSPPYG00000015238
• Aliases: None
• Description: MLF1 interacting protein [Source:HGNC Symbol;Acc:21348]

Sequence

>retro_pabe_979
TCAAAGAACATTTTATGAAGAACACATTCTGTGAAAGATAAAGCTGGTCAAAAGTGCAAGCCTATCAATGTGTTTGATTT
TCCTAATAATTCTGCCATCTCAAGAATTGGCAGGCTTGGTGAAAATGAGAAAGATGAAGAACCTTATGAAACCTTTGATC
CTCCTTTACACAGCTCATCTATGTATGCCAATGAAGAATTCTCCAAATATTGTGGATTATCTATCACTTCAACTCCTCCA
GGAAAAAGAAGCAAAAAGGAGCTCGAGCACTTCTGCAAATGAAGAAAGTGAAAACGAATCTGCAAAAATGAGTGCAAAAA
GCCAGGAAGAAAACTCAAACTCATTAGCGATGAGTCTGAAAGCACTGAAGAAAGTGATGTGAGAAGAAAAGTTAAGTCAG
TGGAGAAAATAAGGACCCAACAACACGAGGCTATTCCAACTACAGCATCTTCAGCCCTTTCAGAGAAACCAGCTGACTCA
GTCACTTCCAAAAAGATAGGACCCATTAGTGACCAGCCATCTGTTGAAAAAGACACACTGACAACAGAAAGTCAAGCAGA
AGCCAGAAAAAAAGGGAATACATCTCATGGCAAAAGGAAGAAATCAAGAAGTGAAGCAATAGACTAAGGTATTTCCAACA
TTGTGCATATTTGGTGTCTGGAAGGAAAGAAAACCAGCGACATCATGGAATTGAATATTGTTTTGCCTGCATTTGAGAAA
ATCCTCGTCCAGTATAAACATAGAATAGAATCTAAAATTTGTAAGAAACACATCAATAAATTTTATTTTACTAGTAAAGA
ACAACTCAACAAAATGCTTAAAAACTCCAGATATTGAAAAATCTGAAAAAGAAGAATGCTAAGGTAATTTCAGATATCAA
AAAGAAATGACAGTGTTTGACTGAAGTCCAGGATGAGCTGCTTTGGTTACAGCCACCAACTGAAACAACTACAAACAAAG
TATTATGAACTTAAGGAGAGAACAGTCTTCCCTTAGGAATGCAGCTATTTCTTATCTAATTCAAAACAGCTCCATCGGAA
GTATTCAGATGTTCAGGAGAAAGAACCAAACGTAAAGGAAACATAAGATTCATCCAGCCTTCCAGGTGTTATTTAAAGCA
GGAACACTTTTGGGAGCTGAAAACCTTCTGTAAAATATCAGCCATCAATGGGAGAAGCTCCTC

Alignment

ORF - retro_pabe_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.73 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SKHTLERMHSMKDKAGQKCKPIDVFDFPDDSDVSSIGRLGENEKDEEPYETFDPPLHSTAIYADEEEFSK
          SK..L.R.HS.KDKAGQKCKPI.VFDFP..S..S.IGRLGENEKDEEPYETFDPPLHS...YA.EE.FSK
Retrocopy SKNIL*RTHSVKDKAGQKCKPINVFDFPNNSAISRIGRLGENEKDEEPYETFDPPLHSSSMYANEE-FSK

Parental  HCGLSIPSTPPGK-EAKRSSDTFGNEASEIESVKISAK-KPGRKLRPISDNSESTEESDTRRKVKSAEKI
          .CGLSI.STPPGK.EAKRSS.T..NE.SE.ES.K.SAK.KPGRKL..ISD.SESTEESD.RRKVKS.EKI
Retrocopy YCGLSITSTPPGK>EAKRSSSTSANEESENESAKMSAK<KPGRKLKLISDESESTEESDVRRKVKSVEKI

Parental  STQRHEVIRTTASSELSEKPAESVTSKKTGPLSAQPPVEKENLAIESQSKTQKKGKISHDKRKKSRSKAV
          .TQ.HE.I.TTASS.LSEKPA.SVTSKK.GP.S.QP.VEK..L..ESQ....KKG..SH.KRKKSRS.A.
Retrocopy RTQQHEAIPTTASSALSEKPADSVTSKKIGPISDQPSVEKDTLTTESQAEARKKGNTSHGKRKKSRSEAI

Parental  GSDTSDIVHVWCPEGMKTSDIKELNIVLPEFEKTHLEQKQRIESKVCKAAIDTFYFNVKEQLTKMLKES-
          ....S.IVH.WC.EG.KTSDI.ELNIVLP.FEK.....K.RIESK.CK..I..FYF..KEQL.KMLK.S.
Retrocopy D*GISNIVHIWCLEGKKTSDIMELNIVLPAFEKILVQYKHRIESKICKKHINKFYFTSKEQLNKMLKNS<

Parental  EMLKNLKRKNAKMISDTEKKRQRMIEVQDELLRLEP-QLKQLQTKYDELKER-KSSLRNAA-YFLSNLKQ
          ..LKNLK.KNAK.ISD..KK.Q...EVQDELL.L.P.QLKQLQTKY.ELKER..SSLRNAA.YFLSN.KQ
Retrocopy QILKNLKKKNAKVISDIKKK*QCLTEVQDELLWLQP>QLKQLQTKYYELKER>QSSLRNAA<YFLSNSKQ

Parental  LYQDYSDVQVQEPNIKETYDSSSLPALLFKARTLLGA-ESHLRNINHQLEKLL
          L...YSDVQ..EPN.KET.DSSSLP......R...G..E..L.NI.HQ.EKLL
Retrocopy LHRKYSDVQEKEPNVKET*DSSSLPGVI-*SRNTFGS>ENLL*NISHQWEKLL

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	0.06 RPM	0.55 RPM
SRP007412_cerebellum	0.12 RPM	0.85 RPM
SRP007412_heart	0.03 RPM	0.51 RPM
SRP007412_kidney	0.17 RPM	0.63 RPM
SRP007412_liver	0.00 RPM	0.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_979 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_979 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151725	1 retrocopy	retro_hsap_1096,
Gorilla gorilla	ENSGGOG00000011892	1 retrocopy	retro_ggor_862,
Microcebus murinus	ENSMICG00000013084	1 retrocopy	retro_mmur_836,
Macaca mulatta	ENSMMUG00000012176	1 retrocopy	retro_mmul_850,
Nomascus leucogenys	ENSNLEG00000010967	1 retrocopy	retro_nleu_1628,
Oryctolagus cuniculus	ENSOCUG00000003903	1 retrocopy	retro_ocun_1174,
Pongo abelii	ENSPPYG00000015238	1 retrocopy	retro_pabe_979 ,
Pan troglodytes	ENSPTRG00000016643	1 retrocopy	retro_ptro_697,