RetrogeneDB ID: retro_pabe_3487

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:73175823..73176546(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNGR2
• Ensembl ID: ENSPPYG00000008684
• Aliases: None
• Description: synaptogyrin 2 [Source:HGNC Symbol;Acc:11499]

Sequence

>retro_pabe_3487
GGGGCCTATGGCGCTGCCAAAGGCGGGCGGCTCCTTCCACCTGCGGGCGCTTCCTGACGCAACCGCAGGTGGTGGTGCGC
GCTGCGTGCAGGGTCTTCGCCTTGATCGTGTTCTCCTACATCTATGATGAGGGCTACAGCAAGTCTAAGCAGAGGTACTG
CGTGTTCAACCACAACGAGGACGCCTGCCGCTACAGCAATGCCATCAGGGTGCTGGCCTTCCAGGCCTCGGTCTTCTTGG
TGGTCGACGCGTATTTCCCCCAGATCAGCAATGCCACTGACCGCAAGTACCTGGTCGTGGGTGACATGCTCTTCTCGGCT
CTCTGAGCCTTCCTGTGGTTTGTTGGTTTCTGCTTCCTCACTAACCAGTGGGCGGCCACCCAACCGGAGGACGTGCTGGT
GGGGGCCAACTCCGCGCAGGCAGCCATCACCTTCAGCTTCTTTTCCATCTTCTCCTGGGGCATGCTGGCTTTCCTGGCCT
ACCGGCACTACAAGGCTGGCGTGGACTGCATCCAGAACTACGTCGACTCCACCCCGGACACCAACACTGCCTACGCCTCC
TACCCAGGTGCATCTGTGGACAACCACCAGCATCTGCCCTTCACCCAGAATGCGGAGACCACTGAGGGCTACCAGCCGCC
CCTTGTGTACTGAGTGGCTGAGTGCCGTTCGGGGTGGGAAGGGGGTGCAGAGAGGACCCTCCCCTCTGCCCTGGACTTTC
CCA

Alignment

ORF - retro_pabe_3487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.03 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAYGAAK-AGGSFDLR-RFLTQPQVVARAVCLVFALIVFSCIYGEGYSNAHESKQMYCVFNRNEDACRYG
          GAYGAAK.AGGSF.LR.RFLTQPQVV.RA.C.VFALIVFS.IY.EGYS....SKQ.YCVFN.NEDACRY.
Retrocopy GAYGAAK>AGGSFHLR>RFLTQPQVVVRAACRVFALIVFSYIYDEGYS---KSKQRYCVFNHNEDACRYS

Parental  SAIGMLAFLASAFFLVVDAYFPQISNATDRKYLVIGDLLFSALWTFLWFVGFCFLTNQWAVTNPKDVLVG
          .AI..LAF.AS..FLVVDAYFPQISNATDRKYLV.GD.LFSAL..FLWFVGFCFLTNQWA.T.P.DVLVG
Retrocopy NAIRVLAFQASV-FLVVDAYFPQISNATDRKYLVVGDMLFSAL*AFLWFVGFCFLTNQWAATQPEDVLVG

Parental  ADSARAAITFSFFSIFSWGVLASLAYQRYKAGVDDFIQNYVDPTPDPNTAYASYPGASVDNYQQPPFTQN
          A.SA.AAITFSFFSIFSWG.LA.LAY..YKAGV.D.IQNYVD.TPD.NTAYASYPGASVDN.Q..PFTQN
Retrocopy ANSAQAAITFSFFSIFSWGMLAFLAYRHYKAGV-DCIQNYVDSTPDTNTAYASYPGASVDNHQHLPFTQN

Parental  AESTEGYQP-TLCTEWRLGWEGG---QRGPSPLPWTFP
          AE.TEGYQP..LCTEW.....GG...QRGPSPLPWTFP
Retrocopy AETTEGYQP>PLCTEWLSAVRGGKGVQRGPSPLPWTFP

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	9.51 RPM
SRP007412_cerebellum	0.00 RPM	9.12 RPM
SRP007412_heart	0.00 RPM	22.43 RPM
SRP007412_kidney	0.00 RPM	57.38 RPM
SRP007412_liver	0.00 RPM	34.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3487 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3487 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1200

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108639	2 retrocopies	retro_hsap_1472, retro_hsap_4275,
Macaca mulatta	ENSMMUG00000021864	1 retrocopy	retro_mmul_1200,
Pongo abelii	ENSPPYG00000008684	2 retrocopies	retro_pabe_1220, retro_pabe_3487 ,
Ictidomys tridecemlineatus	ENSSTOG00000006834	1 retrocopy	retro_itri_705,