RetrogeneDB ID: retro_ggor_2254

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:48609022..48610033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSGGOG00000011022
• Aliases: None
• Description: None

Sequence

>retro_ggor_2254
GAGCAGACCGCCGGCAACCTCCTCTACACCACGCCGCAGGGACCCTCCAGCAGAGCCGGGCTGCTGCAGCCACCAGCGCT
GGGACGAGGCGGCAGTGGCCCTCTGGCAAAGTGAAGTCTGGAGCTAGGAGAAAGCGGTCATCAGTACCTCTCAGATGGTT
CAAAAACCCCCAAGGGCAAAGGAAGAGCTGCACTAAGAGGTCCAGATACTCCAAAAACTCCAAAATCTACCTCAGAAAAA
ACACGGTACAATAGTCTCTTGATCTGCTCACCAAGAAGTTCATTCAGCTCCTGAGCCAGTCACCCGATGGGGTCTTGGTT
TTGAACAAGGCAGCGGAAGTGCTAAAAGTGCAAAATAGAAGGATTTATGATATCACCAACGCTCTGGAAGGCATCCACCT
CATTAAGAAGAAGTCTAAAAATAACGTCCAGTGGATGGGTTGCAGTCTGTCTGCGGATGGGGGCATGCTGACCCAGTGTC
AAGGCCTGTCAAAAGAAATGACCAAGCTCACTCAGGAAGAGAAGAAATTAGATGAACTGATCCAAAGCTGCACCCTGGAC
CTCAAACTATTAACCGAGGGTTCAGATCGTCAAAGGTTAGCTTACGTTACATATTAACATATTCGAAAAATTAGTGGCCT
TAAAGACCAAACTGTTATAGTTGTGAAAGCCCCTCCAGAAATAAAACTCGAGTGCCTGACTCAATAAGAGAGCCTACAAA
TACATTTGGCGGGTACCCAAGGGCCCATTGAGGTTTACTTATGTCCAGAAGAGACTGAAACACAGTCCAATGACAACAAA
CAACCAAGACCCCAATGGGAATATCCTTAAACCCACCTCGTTGGCTTCAACCAACTCAGGACATAGCGATTGCTCAATTT
CTATGGGAAACCTTTCTCCTCTGGCCTCCCCAGCCAACCTCTTACAGCAGACTGCGGACCAAATTCCTTCTAATCCTCTA
GTATGACCATCTGTGAACTTACTGCCTCCCCTGCTGCAAGATGACCATTTG

Alignment

ORF - retro_ggor_2254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.95 %
• Parental protein coverage: 84.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EQTAGSLLYTTPHGPSSRAGLLQQPPALGRGGSGGGGGPPAKRRLELGESGHQYLSDGLKTPKGKGRAAL
          EQTAG.LLYTTP.GPSSRAGLLQ.PPALGR....GG.GP.AK..LELGESGHQYLSDG.KTPKGKGRAAL
Retrocopy EQTAGNLLYTTPQGPSSRAGLLQ-PPALGR----GGSGPLAK*SLELGESGHQYLSDGSKTPKGKGRAAL

Parental  RSPDSPKTPKSPSEKTRYDT-SLGLLTKKFIQLLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHL
          R.PD.PKTPKS.SEKTRY...SL.LLTKKFIQLLSQSPDGVL.LNKAAEVLKVQ.RRIYDITN.LEGIHL
Retrocopy RGPDTPKTPKSTSEKTRYNS<SLDLLTKKFIQLLSQSPDGVLVLNKAAEVLKVQNRRIYDITNALEGIHL

Parental  IKKKSKNNVQWMGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVT
          IKKKSKNNVQWMGCSLS.DGGML.QCQGLSKE.T.L.QEEKKLDELIQSCTLDLKLLTE.S..QRLAYVT
Retrocopy IKKKSKNNVQWMGCSLSADGGMLTQCQGLSKEMTKLTQEEKKLDELIQSCTLDLKLLTEGSDRQRLAYVT

Parental  YQDIRKISGLKDQTVIVVKAPPETRLE-VPDSI-ESLQIHLASTQ-GPIEVYLCPEETETHSPMKTNNQD
          Y..IRKISGLKDQTVIVVKAPPE..LE.VPDSI.ESLQIHLA.TQ.GP............HSPM.TNNQD
Retrocopy Y*HIRKISGLKDQTVIVVKAPPEIKLE<VPDSI>ESLQIHLAGTQ>GPLR-FTYVQKRLKHSPMTTNNQD

Parental  HNGNIPKPASKDLASTNSGHSDCSISMGNLSPLASPANLLQQTEDQIPSN-LEGPFVNLLPPLLQEDYL
          .NGNI.KP.S..LASTNSGHSDCSISMGNLSPLASPANLLQQT.DQIPSN.L..P.VNLLPPLLQ.D.L
Retrocopy PNGNILKPTS--LASTNSGHSDCSISMGNLSPLASPANLLQQTADQIPSNPLV*PSVNLLPPLLQDDHL

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	0.05 RPM	11.75 RPM
SRP007412_cerebellum	0.04 RPM	1.42 RPM
SRP007412_heart	0.00 RPM	1.34 RPM
SRP007412_kidney	0.00 RPM	12.35 RPM
SRP007412_liver	0.03 RPM	3.32 RPM
SRP007412_testis	0.00 RPM	5.70 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_2254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2254 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1749
Pan troglodytes	retro_ptro_1217
Pongo abelii	retro_pabe_1447

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416, retro_chof_871,
Homo sapiens	ENSG00000112242	1 retrocopy	retro_hsap_1749,
Gorilla gorilla	ENSGGOG00000011022	2 retrocopies	retro_ggor_1796, retro_ggor_2254 ,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457,