RetrogeneDB ID: retro_pabe_1447

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:30256547..30257731(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSPPYG00000016269
• Aliases: None
• Description: E2F transcription factor 3 [Source:HGNC Symbol;Acc:3115]

Sequence

>retro_pabe_1447
ATCCTCACCACGAACACTTCCACCACCTCCTGTTCCTCCTCCCTCCAAAGCGGCGCCGTAGCCACCGGCCCCCTCCCCCC
CAGTGCCCCAGGCGCGGAGCAGACCGCCGGCAGCCTCCTCTACACCACGCCCCACGGACCCTCCAGCAGAGCAGGGCTGC
TGCAGCTACCAGCGCTGGGACGCAGCGGCAGCGGCCCTCTGGCAAAGCGAAGACTGGAGCTAGGAGAAAGCGGTCATCGG
TACCTCTCAGATGGTTTAAAAACCCCCAAGGGCAAAGGAAGAGCTGCACTAAGAAGTCCAGATACTCCAAAAACTCCAAA
ATCTACCTCAGAAAAAACGCGGTACGATAGTCACTTGATCTGCTCACCAAGAAGTTCATTCAGCTCCTGAGCCAGTCACC
CGATGGGGTCTTGGTTTTGAGCAAGGCAGCGGAAGTGCTAAAAGTGCAAAATAGAAGGATTTATGATATCACCAACGCTC
TGGAAGGCATCCACCTCATTAAGAAGAAGTCTAAAAATAACGTCCAGTGGATGGGTTGCAGTCTGTCTGCGGATAGGGGC
GTGCTGGCCCAGTGTCAAGGCCTGTCAAAAGAAATGACCGAGCTCAGTCAGGAAGAGAAGAAATTAGATGAACTGATCCA
AAGCTGCACCCTGGACCTCAAACTATTAACCGAGGATTCAGATCGTCAAAGGTTAGCTTACGTTACATATCAACATATTC
GAAAAATTAGTGGCCTTAAAGACCAAACTGTTACAGTTGTGAAAGCCCCTCCAGAAATAAGACTTGAAGTGCCTGACTCA
ATAAGAGCCTACAAATATATTTGGCAGGTACCCAAGGGCCCACTGAGGTTTACTTATGTCCAGAAGAGACTGAAACACAG
TCCAATGACAACAAACAACCAAGACCACAATGGGAATATTCTTAAACCCACCTTGTTGGCTTCAACCAACTCAGGACATA
GCGATTGTTCAATTTCTATGGGAAACCTTTCTCCTCTGGCTTCCCCAGCCAACCTCTTACAGCAGACTGAGGACCAAATT
TCTTCTAACCTAGGATGACCATTTGTGAACTTACTGCCTCCCCTGCTCCTCCTCCTGAGCCTTGGGGAGGAAGAAGGCAT
CAGCCATCTCTTTGATGCTTATGATTTGGAAAAGCTCCCACTGGTGGAAGACTTCATGTGTAGT

Alignment

ORF - retro_pabe_1447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 95.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ILTTNTSTTSCSSSLQSGAVAAGPLLPSAPGAEQTAGSLLYTTPHGPSSRAGLLQQPPALGRGGSGGGGG
          ILTTNTSTTSCSSSLQSGAVA......SAPGAEQTAGSLLYTTPHGPSSRAGLLQ.P.ALGR.....G.G
Retrocopy ILTTNTSTTSCSSSLQSGAVATXXXXXSAPGAEQTAGSLLYTTPHGPSSRAGLLQLP-ALGRS----GSG

Parental  PPAKRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDT-SLGLLTKKFIQLLSQSP
          P.AKRRLELGESGH.YLSDGLKTPKGKGRAALRSPD.PKTPKS.SEKTRYD..SL.LLTKKFIQLLSQSP
Retrocopy PLAKRRLELGESGHRYLSDGLKTPKGKGRAALRSPDTPKTPKSTSEKTRYDS<SLDLLTKKFIQLLSQSP

Parental  DGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQWMGCSLSEDGGMLAQCQGLSKEVTELSQ
          DGVL.L.KAAEVLKVQ.RRIYDITN.LEGIHLIKKKSKNNVQWMGCSLS.D.G.LAQCQGLSKE.TELSQ
Retrocopy DGVLVLSKAAEVLKVQNRRIYDITNALEGIHLIKKKSKNNVQWMGCSLSADRGVLAQCQGLSKEMTELSQ

Parental  EEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRKISGLKDQTVIVVKAPPETRLEVPDSI-ESLQI
          EEKKLDELIQSCTLDLKLLTEDS..QRLAYVTYQ.IRKISGLKDQTV.VVKAPPE.RLEVPDSI..SLQI
Retrocopy EEKKLDELIQSCTLDLKLLTEDSDRQRLAYVTYQHIRKISGLKDQTVTVVKAPPEIRLEVPDSI<KSLQI

Parental  HLASTQ-GPIEVYLCPEETETHSPMKTNNQDHNGNIPKPASKDLASTNSGHSDCSISMGNLSPLASPANL
          .LA.TQ.GP............HSPM.TNNQDHNGNI.KP....LASTNSGHSDCSISMGNLSPLASPANL
Retrocopy YLAGTQ>GPLR-FTYVQKRLKHSPMTTNNQDHNGNILKPTL--LASTNSGHSDCSISMGNLSPLASPANL

Parental  LQQTEDQIPSNLEGPFVNLLPPLLQEDYLLSLGEEEGISDLFDAYDLEKLPLVEDFMCS
          LQQTEDQI.SNL..PFVNLLPPLL....LLSLGEEEGIS.LFDAYDLEKLPLVEDFMCS
Retrocopy LQQTEDQISSNLG*PFVNLLPPLL---LLLSLGEEEGISHLFDAYDLEKLPLVEDFMCS

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	4.26 RPM
SRP007412_cerebellum	0.00 RPM	1.70 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.00 RPM	2.65 RPM
SRP007412_liver	0.03 RPM	1.65 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1447 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1447 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1749
Pan troglodytes	retro_ptro_1217
Gorilla gorilla	retro_ggor_2254

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 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	ENSPPYG00000012646	1 retrocopy	retro_pabe_1,
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,