RetrogeneDB ID: retro_ecab_669

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 27:2600323..2600778(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000020024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSECAG00000021136
• Aliases: None
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_ecab_669
GTGTGGGCGAGTGGAGACAGACTGACCTGGGCAGCGAAGGTGCTGGAGCAGCTCACTGGCCAGACTCTAGTGTTCTCCAA
AGCTAGATACACCAGCAGATCCTTTGGCATCAGAAAAATGAGAAGATTGGCATCCACTGTGCAGGCCATGGGACAAGGCA
GAAGAAATCTTGGAGAAAGGTCTAAAGGTGTGAGTACAAGTTAAGAAGAAATAACTTCTCAGATACCAGAAACTTGGGTT
TGGAGATTCAGGAACACATCAATCCGGGGATCAAATATGACCCGAGCACTGGTATCTGTGAGCTGGACTTCTATGTGGTG
CTGGGTAGGCCAGGTTTTAGCATTGCAGACAAGAAGTGCAGGACAGCTGCACTGGAGCCAAACACAGAATCAGCAAAGAG
CGAGGCCACGTGCTGGTTCCAGCGGAGGTATGATGGCATCATCCTTCCTGGCAAA

Alignment

ORF - retro_ecab_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 85.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRR-NEKIAVHCTVRGAKAEEILEKGLKVREYEL
          V..SGDRLT.AAKVLEQLTGQT.VFSKARYT.RSFGIR..NEKI..HC...G........K.....EY.L
Retrocopy VWASGDRLTWAAKVLEQLTGQTLVFSKARYTSRSFGIRK<NEKIGIHCAGHGTRQKKSWRKV*RC-EYKL

Parental  RKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRT-GCIGAKHRISKE-EA
          R.NNFSDT.N.G..IQEHI..GIKYDPS.GI..LDFYVVLGRPGFSIADKK.RT..C.GAKHRISKE.EA
Retrocopy RRNNFSDTRNLGLEIQEHINPGIKYDPSTGICELDFYVVLGRPGFSIADKKCRT<SCTGAKHRISKE>EA

Parental  MRWFQQKYDGIILPGK
          ..WFQ..YDGIILPGK
Retrocopy TCWFQRRYDGIILPGK

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
SRP021940_articular_cartilage	0.12 RPM	774.00 RPM
SRP021940_cerebellum	0.10 RPM	267.24 RPM
SRP021940_embryo	0.28 RPM	592.49 RPM
SRP021940_placental_villous	0.19 RPM	363.00 RPM
SRP021940_synovial_membrane	0.66 RPM	552.47 RPM
SRP021940_testis	0.00 RPM	263.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_669 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005058	1 retrocopy	retro_acar_165,
Ailuropoda melanoleuca	ENSAMEG00000009704	3 retrocopies	retro_amel_1123, retro_amel_1754, retro_amel_234,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Cavia porcellus	ENSCPOG00000008432	2 retrocopies	retro_cpor_261, retro_cpor_788,
Equus caballus	ENSECAG00000021136	3 retrocopies	retro_ecab_471, retro_ecab_669 , retro_ecab_926,
Felis catus	ENSFCAG00000028651	2 retrocopies	retro_fcat_1069, retro_fcat_1877,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Myotis lucifugus	ENSMLUG00000008868	3 retrocopies	retro_mluc_1271, retro_mluc_1345, retro_mluc_2321,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Otolemur garnettii	ENSOGAG00000032741	6 retrocopies	retro_ogar_1325, retro_ogar_1935, retro_ogar_1963, retro_ogar_2322, retro_ogar_2630, retro_ogar_569,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sarcophilus harrisii	ENSSHAG00000006767	1 retrocopy	retro_shar_638,
Tursiops truncatus	ENSTTRG00000016115	4 retrocopies	retro_ttru_1525, retro_ttru_1779, retro_ttru_476, retro_ttru_911,