RetrogeneDB ID: retro_pabe_1220

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:26181867..26182500(+)
• Located in intron of: ENSPPYG00000006284

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_1220
GTCTTCGCCTTAATCGTGTTCTCCTGCATCTATGGCGAGGGCTACAGCAACGCCCATAAGTCTAAGCAGATGTACCGCGT
GTTCAACCACAACGAGGATGCCTGCCGCTGTGGCAGTGCCATCGGGGTGCTGGCCTTCCCGGCCTCGGCCTTCTTCTTGG
TGGTCGACGCGTATTTCCCCCAGATCAGCAACGCCACTGACCGCAAGCACCTCGTCATTGGTGACCTGCTCTTCTCAGCT
CTCTGGCCCTTCCTGTGGCTTGTTGGTTTCTGCTTCCTCCCCAACCAGTGGGCGGTCACCGACCCGGAGGACGTGCTGGT
GGGGGCCGGCTCTGCGAGGGCAGCCATCACCTTCAGCTTCTTTTCCATCTTCTCCTGGGGTGTGCTGGCCTCCCTGGCCT
ACCAGCGCTACAAGGCTGGCGTGGACGACTTCACCCAGAACTACGTCGACCCCACTCCGGACCCCAACACCGCCTACGCC
TCCTACCCGGGTGCATCTGCGGACAGCTACCAACACCCTTCACCCAGAATGCGGAGAGCACCGAGGGCTACCAGCCGCCC
CCTGTGTACTGAGTGGCGGTTAGGGTGGGAAGGGGGACAGAGAGGGCCCTCCCCTCTGCCCTGGACTTTCCCA

Alignment

ORF - retro_pabe_1220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 86.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFALIVFSCIYGEGYSNAHESKQMYCVFNRNEDACRYGSAIGMLAFLASAFFLVVDAYFPQISNATDRKY
          VFALIVFSCIYGEGYSNAH.SKQMY.VFN.NEDACR.GSAIG.LAF.ASAFFLVVDAYFPQISNATDRK.
Retrocopy VFALIVFSCIYGEGYSNAHKSKQMYRVFNHNEDACRCGSAIGVLAFPASAFFLVVDAYFPQISNATDRKH

Parental  LVIGDLLFSALWTFLWFVGFCFLTNQWAVTNPKDVLVGADSARAAITFSFFSIFSWGVLASLAYQRYKAG
          LVIGDLLFSALW.FLW.VGFCFL.NQWAVT.P.DVLVGA.SARAAITFSFFSIFSWGVLASLAYQRYKAG
Retrocopy LVIGDLLFSALWPFLWLVGFCFLPNQWAVTDPEDVLVGAGSARAAITFSFFSIFSWGVLASLAYQRYKAG

Parental  VDDFIQNYVDPTPDPNTAYASY-PGASVDNYQQPPFTQNAESTEGYQP-TLCTEWRLGWEGGQRGPSPLP
          VDDF.QNYVDPTPDPNTAYASY.PG.........PFTQNAESTEGYQP..LCTEWRLGWEGGQRGPSPLP
Retrocopy VDDFTQNYVDPTPDPNTAYASY<PGC-ICGQLPTPFTQNAESTEGYQP>PLCTEWRLGWEGGQRGPSPLP

Parental  WTFP
          WTFP
Retrocopy WTFP

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	9.51 RPM
SRP007412_cerebellum	0.24 RPM	9.12 RPM
SRP007412_heart	0.21 RPM	22.43 RPM
SRP007412_kidney	0.99 RPM	57.38 RPM
SRP007412_liver	0.49 RPM	34.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1220 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1220 has 0 orthologous retrocopies within eutheria group .

---

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,