RetrogeneDB ID: retro_amel_683

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192567.1:443951..444589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOSPD1
• Ensembl ID: ENSAMEG00000001304
• Aliases: None
• Description: motile sperm domain containing 1 [Source:HGNC Symbol;Acc:25235]

Sequence

>retro_amel_683
ATGCATCAACAAAAAAGACAGCCAGAGTTGGTGGAAGGAAATCTTCCTATTTTTGTGTTTCCCACGGAGCTAATATTTTA
TGCAGATGACCAGTCAACACATAAGCGAGTGTTGACTCTGTATAACCCCTATGAGTTTGCCTTAAAGTTCAAAGTTTTGT
GTACTACTCCAAATAAGTATGTTGTCACTGATGCTGCAGGCGCAGTAAAACCTCAGTGTTGTGTAGATATTGTGATTCGT
CATAGAGATGTTCAATCCTGTCACTATGGTGTAAAAGACAAGTTCCGCCTCCAAATTTCCGAGCAGAGCCAGGGGAAAAC
TTTAGGAAGGAAAGAGGTTGTGGCTATTCTTCACCCATCTGCAAAAGAACAACAAAAGGAAGAAGAGGAAAAAAGGATAA
AGGAACACTTAACTGAAAGTTTATTTTTGAGCAGTCCTTTCAACCAGAGAACAGAGCTGTCTCCTCAGGACCTAGCTTAC
TAACCATCTTCCTGGGAGTGGTGTGCATTGCAGCTTTGATGCTTCCTTCGCTCGGGGCTGTGGAATCGCTGGTACCTCTC
TTTCTCTACTTAAGTGTGAATCAAAAATTAGTGGCTGCTTATGTCTTAGGTCTTATCACAATGGCTATACTTGGAACA

Alignment

ORF - retro_amel_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHQQKRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVADAAGAVK
          MHQQKRQPELVEGNLP.FVFPTELIFYADDQSTHK.VLTLYNPYEFALKFKVLCTTPNKYVV.DAAGAVK
Retrocopy MHQQKRQPELVEGNLPIFVFPTELIFYADDQSTHKRVLTLYNPYEFALKFKVLCTTPNKYVVTDAAGAVK

Parental  PQCCVDIVIRHRDVQSCHYGVKDKFRLQVSEQSQRKALGRKEVVAILHPSAKEQQKEEEEKRIKEHLTES
          PQCCVDIVIRHRDVQSCHYGVKDKFRLQ.SEQSQ.K.LGRKEVVAILHPSAKEQQKEEEEKRIKEHLTES
Retrocopy PQCCVDIVIRHRDVQSCHYGVKDKFRLQISEQSQGKTLGRKEVVAILHPSAKEQQKEEEEKRIKEHLTES

Parental  LF-FEQSFQPGKNRAVSSGPSLLTIFLGVVCIAALMLPTLGDVESLAPLYLHLSVNQKLVAAYILGLITM
          LF.FEQSFQP..NRAVSSGPSLLTIFLGVVCIAALMLP.LG.VESL.PL.L.LSVNQKLVAAY.LGLITM
Retrocopy LF<FEQSFQP-ENRAVSSGPSLLTIFLGVVCIAALMLPSLGAVESLVPLFLYLSVNQKLVAAYVLGLITM

Parental  AILRT
          AIL.T
Retrocopy AILGT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_683 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_683 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001304	1 retrocopy	retro_amel_683 ,
Choloepus hoffmanni	ENSCHOG00000007386	5 retrocopies	retro_chof_1202, retro_chof_1623, retro_chof_201, retro_chof_2295, retro_chof_675,
Dasypus novemcinctus	ENSDNOG00000013117	4 retrocopies	retro_dnov_1825, retro_dnov_2650, retro_dnov_2660, retro_dnov_926,
Macaca mulatta	ENSMMUG00000022505	1 retrocopy	retro_mmul_133,
Monodelphis domestica	ENSMODG00000015178	1 retrocopy	retro_mdom_159,
Mus musculus	ENSMUSG00000023074	1 retrocopy	retro_mmus_291,
Otolemur garnettii	ENSOGAG00000005739	2 retrocopies	retro_ogar_2508, retro_ogar_528,
Sarcophilus harrisii	ENSSHAG00000011544	1 retrocopy	retro_shar_21,
Sus scrofa	ENSSSCG00000012686	1 retrocopy	retro_sscr_690,
Ictidomys tridecemlineatus	ENSSTOG00000008152	1 retrocopy	retro_itri_1303,
Tarsius syrichta	ENSTSYG00000006102	1 retrocopy	retro_tsyr_1785,